"We don't require our food to agree with us."Stargate Atlantis is a spin-off of the popular sci-fi show Stargate SG-1.SG-1 spent its seventh season searching for a "lost city", which they believed was actually a ship belonging to the Ancients. Finding a way to travel to the city via a very long Stargate jump to the Pegasus galaxy, an expedition was put together to assess the new location, what threats it may have and the radical leftover technology there might be.Stargate Atlantis is similar in tone to SG-1, but is successful in distinguishing itself from its predecessor, partly through an intriguing new enemy in the Wraith and through being very much Fish out of Water as they have little actual knowledge of how the city and its technology works. The character dynamics are inverted from its parent show, as Atlantis is a scientific research group with military support. The Mission Commander Elizabeth Weir is a civilian, as are most of the scientists and doctors, with John Sheppard being the head of the military support team.The show branches off from SG-1 after the first episode of season eight, and continues for five seasons. It was continued through a series of tie-in novels.
— Wraith Queen
Stargate Atlantis provides examples of the following tropes:
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- Abandoned Warehouse: Michael uses abandoned warehouses on evacuated worlds through the later seasons to set up his mad science laboratoria and safe houses.
- Action Girl
- Teyla, ascending to Action Mom in season 5.
- Amelia Banks, one of the control room technicians, is well-trained in kickboxing. She starts a relationship with Ronon after he sees her beating up one of Michael's hybrids.
- Affably Evil:
- Todd the Wraith is surprisingly charming and personable for a life-sucking monster (and has a sense of humor — he even makes some jokes that aren't morbid), especially since every other member of his Always Chaotic Evil species seems to lean heavily towards the Large Ham school of Stupid Evil. He shows signs of being a budding Magnificent Bastard, and is honest enough not to pretend to be anything other than a human-eating monster, and is quite frank with the heroes in pointing out that, no matter how many times they cooperate out of necessity, their fundamental nature will inevitably make them enemies at some point (though the Atlantis expedition has begun to take steps to remedy this). Todd can even be said to be trustworthy, as he honors a deal with Sheppard even though Sheppard is completely at his mercy. He's also by far the most pragmatic of the Wraith.
- Wraith in general are pretty agreeable bad guys if you have to have a villain. Their weapons are designed to incapacitate, not kill (so they can eat you, but still), which puts them on the moral high ground compared to your local police department. Their only kill to eat, and it's not their fault humans are their only food source. They sleep for long periods of time (typically several centuries) so whole generations can go by without being oppressed. In the end, they are finally defeated by a fair and balanced truce.
- A.I. Is a Crapshoot: The Replicators - oh and how, several times, caused not only by their original code - as per the trope - but also by the Wraith, and by Atlantis Expedition meddling - see Nice Job Breaking It, Hero! below - over and over and over...
- Alas, Poor Villain: Subverted in "The Prodigal" with Michael. His fight with John Sheppard on top of the Atlantis main tower concludes with Teyla (who's most personally connected to Michael) and John throwing him off it. Michael holds on to the ledge and screams at Teyla for mercy. By this point Michael had already committed galactic genocide, kidnapped and experimented on Teyla's people, mutated her husband into a monster, tried to harvest her baby at least twice, and tried to kill her and everyone in Atlantis out of petty spite. She kicks his hands and watches him fall to his death.
- The Alliance: One episode in Season 4 features a brief alliance between the Atlantis team, several Wraith hives, and the Travelers to destroy the Replicator homeworld. They succeed.
- All There in the Manual: Deleted scenes included on the DVD releases give a lot of supplemental information, and even tentatively conclude several plotlines that reach back to Stargate SG-1. Several producers have explained that, as far as they are concerned, the scenes are canon, but that they are not official since they never made it to air.
- All Your Base Are Belong to Us
- In the first season the Genii seize Atlantis for a brief time after the majority of the expedition evacuates to avoid a dangerous hurricane.
- The Replicators conquer the station (from the Ancients) and plan to return with the city to their homeworld to replace the ship that had been destroyed earlier in the third season.
- Michael seizes the gateroom and operational control of the city for a single episode, but never does manage to seize the entire facility.
- The Wraith pull one at the Midway station, complete with one of them appearing on a computer screen and telling Sheppard that he has no chance of retaking the station.
- Alone Among the Couples: John by the end of the series, as Rodney/Jennifer, Teyla/Kanaan and Ronon/Amelia have all gotten together and his Will They or Won't They? Ship Tease Elizabeth has been turned into a replicator.
- Alternate Reality Episode: "Vegas," the penultimate episode, which features Sheppard as a police detective in the title city chasing a Wraith that crashed on Earth after a failed culling. Mostly a Diabolus ex Machina episode to give an excuse for the Wraith to find Earth in the main reality.
- Always Chaotic Evil: Subverted with the Wraith. At first, they seem worse than the Goa'uld, but then you find out that the only thing they can feed on is humans, and that the 'hunger' feels like "burning alive" in a starvation state. Yes, they do horrendous and horrible things to humans, and their physiology isn't an excuse, but there is a very good reason why they do what they do. It doesn't make them evil by nature. However, there are a lot of Magnificent Bastards among them that would take the skin off your back without a second thought.
- Amazon Brigade: The all-female expedition team from season five episode "Whispers".
- Amazon Chaser: Ronon shows an attraction to, and starts a (minor) relationship with Amelia Banks after he sees her beat up one of Michael's hybrids in "The Prodigal".
- And Man Grew Proud: The pilot reveals that the Greek myth of Atlantis was inspired by the true story of the Ancient city: A great civilization that sank beneath the waves of the ocean. The Greeks simply did not understand that it happened on another planet.
- And Then What?: Todd the Wraith asks the heroes this with regards to their plan to genetically re-engineer the Wraith so that they no longer need to prey upon humans, as it is all that the Wraith have ever known.Dr. Keller: It's for your benefit too. If you don't have to rely on human feeding, the war would be over.
Todd: Perhaps... But then what would we do? Who would we be?
- Arbitrary Skepticism: "The Shrine"; "The Seer". Really, Col. Carter, remember that time you and SG-1 encountered the exact same situation?
- Arson, Murder, and Jaywalking: In a first season episode, Rodney is about to receive gene therapy, prompting the following exchange with Dr. Beckett:Carson Beckett M. D.: (sighs) We believe ATA or Ancient Technology Activation is caused by a single gene that's always on. Instructing various cells in the body to produce a series of proteins and enzymes that interact with the skin, the nervous system and the brain. In this case we're using a mouse retrovirus to deliver the missing gene to your cells.
Dr. Rodney McKay: A mouse retrovirus?
Beckett: It's been deactivated.
McKay: Well, are there any side effects?
Beckett: Dry mouth, headache, the irresistible urge to run in a small wheel...
- Artistic License – Gun Safety: In the episode "Common Ground", during their escape Todd is at one point toying with his loaded gun while having it pointed right at the back of Sheppard's head. Of course this may be deliberate, since an alien from another galaxy is unlikely to have ever learned how to safely handle human-made firearms, especially the Wraith's own handheld weapons stun only. The rest of the series generally averts it, and is very careful about their weapons.
- Ascended Extra: Rodney McKay had a few minor appearances on SG-1 as a rival with pseudo-Unresolved Sexual Tension for Samantha Carter. The character intended to be the smart guy was originally to be called "Ingram" and be black, but was re-written as McKay after David Hewlett joined the cast.
- The Asteroid Thicket: They actually use the game as an expository device when they need to shoot their way through the "edge" of a thicket, and the situation become even worse when they point out how this thicket is actually less dense than the average asteroid field.
- Astronomic Zoom: The opening episode of season 5. The Atlantis team have infiltrated the Michael facility where the kidnapped Teyla will soon be taken to deliver her baby, but a boobytrap triggers and it collapses on top of them. We zoom out from the wreckage all the way into space past planets, stars, and nebulas, until we arrive at Michael's cruiser hovering in orbit over a planet several systems away.
- As You Know: When Woolsey tries it with Ronon, Ronon says that he actually did not know that. Woolsey follows up that he previously explained it personally, but Ronon says he missed that meeting, and Woolsey says that he saw Ronon there.
- Seeing as most of the episodes revolve around highly intelligent characters speaking to each other in fake science, most of the dialogue is made up of this.
- Authority Equals Asskicking: Wraith Queens are generally less physically powerful than their subordinates, although their telepathic skills are usually much stronger. The Wraith 'King' in "Sateda" on the other hand is by far the strongest member of his hive. After Ronon kills off increasingly bigger waves of Wraith hunters and warriors that his enemy sends after him, he taunts him to come down himself. The Wraith takes the challenge, and quickly curbstomps Ronon, forcing Beckett to kill him with a drone weapon. Considering the fierce nature of Wraith society this may even be an inversion, in that he might be King precisely because he's so strong.
- Atlantis: In this series, it's an ancient city-sized spaceship, rather than an ancient mythical continent.
- Notable in that the myth of Atlantis is actually true in the Stargate verse. It's just that noone knew that it happened in another galaxy and aliens were involved. The tale was passed onto the ancient Greeks by surviving Ancients who fled back to Earth through the stargate after sinking and abandoning Atlantis after it came under overwhelming attack by the Wraith.
- Back for the Dead: Lt. Ford is first Put on a Bus, brought back, then Put on a Bus anew and never heard from again for the rest of the series. It is more-or-less implied he did not survive his suicidal gambit to escape the Wraith, even though the door is left open just in case.
- Back from the Dead: Carson Beckett, who dies at the end of season three and returns at the end of season four in clone form.
- Badass in a Nice Suit: To emphasize that it takes place in an alternate universe, "Vegas" has every regular SG character (except Walter Harriman) dressed in a suit instead of their traditional garb. This includes McKay, Keller and even Zelenka. Sheppard also wears a suit throughout the episode, but it is a dirty and disreputable affair to emphasize his squalid lifestyle.
- Badass in Distress
- Sheppard is kidnapped and tortured by Kolya in order to extort Weir's help in toppling the Genii government; he is forced to team up with Kolya's Wraith prisoner (Todd) in order to escape while his team tries to find him.
- In "Sateda", Ronon is re-captured by the Wraith faction that turned him into a runner and is used again as hunting prey. He is saved by the arrival of the Atlantis team and a well-timed puddle jumper.
- Bait-and-Switch Tyrant: Woolsey taking over the command of Atlantis.
- Bare Your Midriff: Teyla in most of her "civilian" clothes.
- Bash Brothers: Ronon and Teal'c... versus the Wraith.
- Battle in the Center of the Mind: The entirety of "The Real World".
- The Battlestar: Wraith Hive ships serve as their main battleships, mobile cities, and carriers for hundreds of dart fighters.
- The 304-class ships from Earth, including the Daedalus and the Apollo.
- Atlantis itself is an intergalactic starship that can defend itself with a powerful shield and Ancient drone weapons, and carries a few dozen Puddle Jumpers that the expedition use as armed scout ships.
- Beach Episode: In the commentary for the first-season episode "Sanctuary", actresses Rachel Luttrell and Tori Higginson discuss the feasibility of having a beach episode. They mention that there must be at least one floor in Atlantis that is at sea-level and whose edge can serve as a boat/swimming dock to stand in for a sand beach. However, they also mention that they are happy that Atlantis lacks an actual beach, because if it did Teyla would probably wind up in a tiny bikini and Elizabeth would be dressed in an all-concealing parka.
- Bee People: The main enemy race, the Wraith, are human-insectoid hybrids whose society is run by queens. They even have hiveships and the queens are usually considered a much bigger foe than the ordinary 'drone' wraith. Oh, they are also life-sucking-sufficiently-advanced-aliens, so that makes them Our Vampires Are Different, too.
- Being Tortured Makes You Evil: The conversion process for creating Wraith worshippers is for the Wraith to drain the human almost to death, only to restore their years at the last second. Repeating this enough times instills complete obedience in the human and makes them quite willing to sacrifice their own kind to the Wraith.
- The process is found to be highly addictive, as those who are 'detoxing' from the process have brain activity that mimics that of a drug addict going through withdrawal from opiates. So more like 'Drugs Make You Evil'.
- Beneficial Disease
- Sheppard is resistant to Lucius Lavin's mind-control pheromones because he has a cold and cannot smell anything.
- When Jeannie, McKay's sister, is infected with nanites that will eventually render her comatose and braindead as they "fix" her epilepsy, McKay buys time to deactivate them by breaking her legs, forcing them to focus on that and keeping them away from her brain.
- Beware the Nice Ones
Elizabeth: If you waste one more minute that could be used to save the people on that ship because of your ego, I promise you I will dial the coordinates of a planet where you can be as self-important as you want to be. You think I'm kidding?
- Elizabeth Weir repeatedly. First demonstrated by her smackdown to Kavanagh in "Thirty-Eight Minutes".
Kavanagh: You wouldn't do that. We'll talk about this later.
Elizabeth: Never again. Now Kavanagh. Get. Back. In. There!
Teyla: If you ever abuse my friendship again, I will not be so forgiving!
- Teyla. After Ronon manipulated her to arrange a meeting in order to assassinate Kell, the man who betrayed thousands of people on Sateda to save himself, Teyla calmly waits until they are in a quiet spot, then slams him against the wall and draws a knife against his throat.
- Big Bad: Several Chief among them are the Wraith (among which no single Wraith has managed to claim the title of overall leader, although Todd managed to get pretty close even though he cooperated with Atlantis more often than against them), but there's also the Asurans (lead by Oberoth), Michael and his Hybrid faction, and the evil Asgard were to be another significant adversary before the cancellation.
- Big Damn Heroes
Sheppard: It was a daring rescue.
- In "Miller's Crossing", Sheppard, Ronon and the NID burst in to save McKay and his sister when they have been kidnapped and she experimented upon.
- In the finale, Carson Beckett pulls this with Atlantis itself.
- Big Eater: McKay, whose hunger and obsessive eating is a frequent point of discussion and even, occasionally, a plot point.
- Bilingual Bonus: Zelenka's Czech is half context-relevant dialogue from the character, and half fourth-wall-breaking commentary from the actor. It is often also an instance of Getting Crap Past the Radar, with more vulgar words than would be acceptable in English.
- Bittersweet Ending: In "Vegas", an alternate John Sheppard lies dying alone in the desert, but his sacrifice actually saved the galaxy.
- Blue and Orange Morality: The Wraith do not really hate humans, it is just a normal predator/prey relationship that looks malevolent when seen from the "prey" side of the line.
- Body-Count Competition: In "Whispers", they know that there were twelve monsters and are trying to figure out how many are left. Sheppard killed one and Sergeant Dusty killed two, which she points out automatically puts her in the lead.
- Body Horror: "The Seed"; "Conversion"
- The Wraith hive ships themselves. They're biological in nature, and made of a mixture of slimy skins, tenticles, and veins. Standing inside one looks a hell of a lot like what would happen if you could stand in a tumour. Worse. One episode actually reveals that the Hive ships were once human when Ronan and another Atlantis operative are infected by Michael, and start to change into hive ships.
- The concept of what happened to Elizabeth and her replicators. Being infected with tons of tiny robots that could be reactivated at any point and used to completely take over your body and mind, effectively killing anything about you thats human? It may be a more psychological form of body horror but still, yikes!
- Boldly Coming
McKay: Oh, how 1967 of you.
- Sheppard, several times, and never without heavy Lampshade Hanging by Rodney:
McKay: Oh, my God! He IS Kirk.
- Later, when McKay (and everyone else) find out that Sheppard really did sleep with the alien in question:
- This gem from "McKay and Mrs. Miller";
- Booby Trap: The Runner in "Tracker" sets up at least three traps in the woods in order to keep himself from being tracked back to the shelter where he has hidden the wounded young girl he is caring for. After Ronon manages to dodge the second trap, he comments that "he's good."
- Bottle Episode: In the commentary for "Hot Zone", writer Martin Gero explains that a benefit of the vast sets constructed for the series is that they can produce bottle episodes (episodes that are filmed entirely on already-constructed sets with a minimum of special effects) that still have the large scope of a regular episode. They specifically mentioned that episode and the preceding "Thirty-Eights Minutes", which still managed to feature several different groups of characters operating in distinct locations.
- Breaking the Fourth Wall
Sheppard: General O'Neill didn't buy it but I think Wolsley did.
- In The Return - Part II
McKay: Well I did win a Sears Drama Fest Award when I was a kid. I could have made it a career if I wanted to.
Sheppard: Wish you would've.
- Brick Joke: In the beginning of "Missing", Keller puts a big container of lollipops in her medical bag, which is quickly lost to the Bola Kai. Later, at least two members of the Bola Kai are seen sucking lollipops.
- Brilliant, but Lazy: When he is not being a Colonel Badass, Colonel Sheppard prefers to do as little work as possible and describes himself as lazy. Some of the show's funnier moments have been other characters reacting to his quick and often out-of-the-box thinking. In the alternate reality belonging to "Rod" McKay, their Sheppard averts this, being both an active member of Atlantis' Mensa chapter and resident Insufferable Genius.
- Sheppard does point out in a throw away line that he has both taken the test for Mensa, and passed. He just didn't feel like joining.
- Broken Pedestal
McKay: That's why the Ancients didn't put it into common use! It's just one more in a long line of abysmal, over-ambitious failures! Oh God. I'm a dead man!
- The Ancients. Over the course of the series you realize how utterly careless and arrogant they were and how badly they screwed up both the Pegasus Galaxy and the Milky Way. Lampshaded by McKay in "The Tao of Rodney" after an accident with an Ancient Device will either cause him to ascend or kill him.
Vanir Leader: Because they did not believe the end justifies the means.
- The Vanir, a rogue faction of Asgard who were trapped in the Pegasus Galaxy after their intergalactic ships were destroyed and willing to do anything to ensure their own survival. When Daniel Jackson and Rodney call them out on their actions, that they're the Asgard and supposed to be the good guys, their response is to point out how well that mentality helped their brethren become extinct in the Milky Way.
Daniel Jackson: Exactly!
Vanir Leader: And look where that got them.
- Bulletproof Human Shield
- Sheppard does it with a Genii in "Common Ground". Apparently, Genii's automatic weapons aren't powerful enough to go through a body.
- Again, when Sheppard is being chased by the Genii in "Remnants" he captures one with a tree snare and hides behind his hanging body while he shoots the other two soldiers.
- Bury Your Gays: The only Atlantis personnel to die in "Whispers" is Captain Vega, who had been implied (in deleted scenes) to be a lesbian.
- California Doubling: Or rather Vancouver, par for the course for Stargate.
- Call-Back: When Colonel Carter is packing her equipment at the SGC in preparation for taking command of Atlantis, Teal'c gives her a farewell speech, which culminates with the statement that "undomesticated equines" (Wild Horses) could not keep him from visiting her. She laughs and says "nice Call-Back;" Teal'c had first referred to horses in such a manner back in season one of Stargate SG-1.
- Cannot Spit It Out: for some reason, members of the Atlantis exhibition are strangely unable to explain about the Ancients and/or their presence in Atlantis whenever a good five to ten minute explanation could solve the plot of the day. Later on in the show this is sometimes justified in that they are dealing with societies they don't trust and are trying to keep their presence on Atlantis a secret, but usually not explaining about the Ancestors only becomes an issue when the people in question know they live in Atlantis anyway. See Poor Communication Kills entry below.
- Captain Smooth and Sergeant Rough: Major Sheppard and Sergeant Bates in the first season. Bates, a Marine non-com, is much more blunt than Sheppard, and spends much of the first season arguing with him over what he sees as too-lenient restrictions on the Athosians, who Bates see as a security risk.
- Casual Danger Dialogue: He is rarely casual about it, keeping with his usual manic and panicked personality, but McKay is frequently sidetracked by random or inane conversations in the midst of high-pressure or dangerous situations. The other members of the team frequently need to remind him that now is not the time to pursue that train of thought.
- Caught with Your Pants Down: In "Grace Under Pressure", Rodney McKay is badly injured and hallucinates seeing his long-time crush, Samantha Carter. Even though he is well aware that she is just a figment of his imagination, he works with "her" to try to help his situation. When "Samantha" comes up with an idea that gives him much-needed extra time, he jumps up and hugs "her". He suddenly turns serious and moves in for an amorous kiss, but "Samantha" spoils the mood by pointing out, "You do realize what you're doing here, right?" Possibly the only example where the person who caught him was actually his own subconscious.
- The Cavalry: "The Siege", the season one finale and season two opener, sees the US Marines arrive to defend Atlantis from Wraith attack, and then the Daedalus arrives to drive off the remaining forces.
- Celebrity Star: The world's greatest physicists are trapped in a building with an Applied Phlebotinum device that is about to kill them all. Said physicists include the director of the Hayden Planetarium and Stephen Hawking. So of course, out of all of them, the one fellow Dr. McKay chooses to help him save the day is Bill Nye the Science Guy. The episode also allows for a Funny Moment when Rodney asks Neil deGrasse Tyson if he has made any children cry today.McKay: Hey, at least I didn't declassify Pluto from planet status. Way to make all the little kids cry, Neil. That make you feel like a big man?
- The Chains of Commanding: Sheppard points out to prospective-queen Harmony that being in charge is not fun and games, and that you need to put the needs of your people ahead of your own essentially all the time.
- Elizabeth bears the brunt of this tropes as the main leader of Atlantis during the series. It's particularly present in the first season when they're cut off from earth and every call is down to her. However when the IOA cast doubts on her position she's more than ready to defend her role and proves that, unlike them, she's willing to take on the responsibilities as leader.
- John struggles with this as Atlantis's second in command and ranking military officer. The few times he has to cover from Elizabeth he's obviously uncomfortable and makes it clear he doesn't want her level of responsibility.
- Characterization Marches On: When Rodney McKay was first introduced on SG-1 he was a much more smug, self-confident character with noted sexism. Starting with the pilot of Atlantis, his general self-confidence transformed into intellectual arrogance and he became more panicked and unsure when it came to women.
- Chekhov's Gun: In "Midway", Ronan and Teal'c find themselves inside a room with a couple of spacesuits. By the end, Sheppard manages to avoid death by entering one of these.
- Chestburster: In "Doppelganger", an alien entity is plaguing the expedition members with vivid nightmares. It does this to Dr. Keller by creating a dream where an Iratus Bug bursts through Teyla's chest and kills her.
- City of Weirdos: "Vegas" points out how very easy it would be for a Wraith to hang out in Las Vegas and have nobody notice. He does disguise himself with prosphetics and punk clothing, but still.
- Climb, Slip, Hang, Climb: Sheppard does it in "Quarantine".
- Clingy MacGuffin: In "Tracker", the Runner Kyrik was in possession of an ancient armband artifact that fused onto him, and allows him to teleport short distances as long as it's powered up.
- Cloning Blues: Carson's clone never knew he was a clone until he managed to make it back to Atlantis.
- Les Collaborateurs: The Wraith regularly wipe out inhabited worlds to feed on the humans. Nevertheless, they also have a few thousand human followers who worship them and are mostly used for infiltration purposes. They're converted by getting fed on repeatedly only to have their lives restored to them. The experience is so traumatic and addictive that they become mindlessly loyal to their Wraith masters. Every other Pegasus human understandably despises them for their treachery.
- Colonel Badass: John Sheppard, Samantha Carter, Steven Caldwell and Abraham Ellis are all Colonels in charge of different aspects of the Atlantis expedition. When they are all in the same room at the same time, Hilarity Ensues.Caldwell: Colonel. (to Ellis)Ellis: Colonel. (to Caldwell)Caldwell: Colonel. (to Carter)Carter: Colonels. (to Ellis and Caldwell)Ellis: Colonel. (to Sheppard)Sheppard:Colonels. (to Ellis and Caldwell)McKay: Seriously?
- Whole scene is here
- Command Roster: Made interesting as various mission commanders take control of the Atlantis expedition, which rearranges the dynamic.
- Conflict Killer: Teyla and Sergant Bates have a growing conflict throughout season one, where Bates believed that Teyla was a security risk that was feeding information to the Wraith, either willingly or subconsciously. This came to a head in "The Siege, Part 1" where they exchanges physical blows after Bates makes an explicit accusation after a mission goes wrong. Later in the episode Bates is discovered beaten so severely that Beckett fells it is best to keep him in a medically-induced coma, attacked by a Wraith that had secretly been in the city for weeks; after the beating he is shipped out of the base for treatment and never returns to Atlantis.
- Colour-Coded for Your Convenience: The Atlantis uniforms are different colours for different divisions. The military are in black, scientists in blue, medical staff in yellow, technicians in green and leaders/civil servants in red. Native allies often wear brown, earthy shades.
- Continuity Nod: In the first episode, while O'Neill and Sheppard are flying to the Ancient outpost in Antarctica, Sheppard mentions a liking for the continent, to which Jack responds that it is his least favorite continent. This makes a lot of sense, considering he and Carter nearly died there several seasons ago in Stargate SG-1 when they were stranded there after a gate malfunction, nearly died again in Season 5 when they unfroze the Ancient plague, and nearly died again in Season 7, first when attacked by Anubis' fleet, then when his head full of Ancient database forced him into cryosleep.
- Continuity Porn: In "Doppleganger", Carter refers to the events of "Cold Lazarus", where they encountered a similar form of Crystal Entity that briefly impersonated Jack O'Neill, "The Gatekeeper" which was where they first acquired Virtual Reality technology, as well as her time being taken over by an alien entity in "Entity".
- Conveniently Empty Building: The shack destroyed by a backwards-held bazooka in "Condemned".
- Cool Gate: It is Stargate Atlantis.
- Courtroom Episode: "Inquisition"
- Crazy Enough to Work: When Martin Gero and Brad Wright were discussing the conclusion to "Hot Zone", the original plan had been for the characters to simply generate an electro-magnetic pulse using equipment in McKay's lab. After realizing that this idea did not have much emotional power, Wright mentioned that nuclear explosions generate an EMP and Gero commented that that was crazy. According to the commentary for the episode, Wright's response was "so crazy it just might work."
- Create Your Own Villain: The Ancients [[spoiler:accidentally created the Wraith, the enemy that drove them out of the Pegasus galaxy and terrorized the galaxy for over 10,000 years.
- The Atlantis Expedition transformed a captured Wraith into a human named Michael, a recurring villain who manages to conquer the galaxy in a Bad Future.
- Critical Staffing Shortage: It varies from the norm in a couple of ways; the new residents of the city are more numerous than usual, probably in the neighborhood of 100 or more, and they are explicitly prepared for an abandoned city, with the best people for the job.
- Cure for Cancer: When McKay and his sister reprogram Replicator nanites, they celebrate it as a possible cure for cancer. Then the nanites kill the person anyway.
- Cute Monster Girl: Elia, the Wraith girl from the episode "Instinct". The unsettling appearance of the life-sucking bug-human hybrid girl can't hide Jewel Staite underneath the facial prosthetics. Her caretaker originally decided to raise her as his daughter because he couldn't bring himself to kill her.
- Deadpan Snarker:
- Hermiod stands out as being the only Asgard we have ever seen to repeatedly snark and express outright annoyance at humanity, especially with McKay.
- Seems to have been a requirement to join the Atlantis expedition, but most of the time it is Sheppard.
- Todd the Wraith is the one Wraith to really seem to enjoy deadpan sarcasm.
- When O'Neill is hiding in Atlantis with Richard Woolsey in The Return Part II, he spends almost all of the first half of the episode exuding this trope.
- Death by Pragmatism: Used with many Shoot the Dog moments.
- Decapitation Presentation: In "The Last Man", Michael does this with the head of a Wraith queen.
- Deconstructed Character Archetype: The series deconstructs the Space People trope with the introduction of the "Travelers." As cool as it sounds to be a people that lives their entire lives on ships in interstellar space, by the time of the show it's proven to be a cultural dead end. Without access to planetary resources they're unable to build new ships. The ships they do have are aging clunkers kept running with scavenged parts, and none of them are replaceable. Their population growth has to be strictly controlled because they only have so much living space. They keep to themselves so much that most other civilizations aren't even aware of their existence, or else consider them untrustworthy scavengers who'll do anything to survive. They are slow to form alliances or expose themselves to situations that could lead to open conflicts, because they have so much to lose. Many have simply abandoned the Traveler lifestyle and integrated themselves into terrestrial societies.
- Defrosting Ice Queen: Atlantis tends to bring out the best in people.
- Woolsey, continuing his arc from SG-1, noticeably lightens up and becomes less bureaucratic from his earlier appearances. Even the producers referred it as "his redemption".
- McKay. Lampshaded in "The Defiant One" where someone points out that he is less insufferable, braver and less self-centered, compared to the cowardly insufferable asshole he used to be in SG-1. Especially evident in the episode "McKay and Mrs. Miller", where McKay finally admits that he does love his sister Jeannie, wants to be part of her life and acknowledges his fault and regret they were estranged for so long.
- Ronon Dex. His homeworld was wiped out, the woman he loved killed in front of him, and he spent several years constantly hunted by the Wraith and socially isolated; he began to lighten up almost as soon as he got a chance to live again and not just survive.
- Deliberately Cute Child: Harmony has Sheppard wrapped around her finger with the proper application of tears and insinuations that McKay is the one who ate his power bar.
- Delivery Guy: McKay to Teyla in the season 5 opener.
- Department of Redundancy Department: When Zelenka explains to Elizabeth that the Ancient computer system is incredibly redundant and difficult to erase, Elizabeth repeats his "redundant" statement right back to him. Zelenka explains how that never gets old.
- Depending on the Writer: Rodney McKay changes personalities constantly for the first 3 Seasons, sometimes competent and worried, sometimes an incompetent whiner, sometimes brave, sometimes a coward, sometimes an egotistical twit who saves the day but won’t shut up. Season Four, he makes the transition to reluctant hero. McKay is the guy that the writers forgot that walked 6+ miles just from the Stargate and back and forth and back for a total of at least 24 miles without breaking a sweat or falling behind, while carrying a heavy rifle, and bearing a full fifty to seventy pounds of field gear in Season Three’s Vengeance — with the writers constantly poking fun at him for being out of shape in dozens of episodes. There are times that you can actually like the guy instead of wanting to sacrifice him on a suicide mission. There are other times... such as when the writers can’t resist bringing back the whiny old Rodney-type from Seasons 1 to 3 to later Seasons in episodes like Season 5’s “the Lost Tribe” after you’ve gotten used to the “new and improved” reluctant hero model that’s had the impurities burned away. It’s like he’s had his reset switch hit, right back to Season One. Poink! Instead of character derailment, it’s more like jumping the tracks at random, for five years running.
- Designated Parents: John and Elizabeth as the leaders of the expedition.
- "Die Hard" on an X: "The Prodigal". The episode even ends with Teyla tossing Michael off the top floor of the Atlantis main tower.
- Digging Yourself Deeper: McKay does it so frequently that listing individual examples here is simply impractical and would take up half the page. Lampshaded in "Trio", where Keller points out that if Carter had not interrupted him, he would have gone on all day.
- Dirty Cop: In "Vegas", Detective John Sheppard barely scrapes by on his performance reviews, has illegal gambling debts, and quits his job to skip town after stealing money from a crime scene.
- Discount Lesbians: Depending on how you count these things, "Duet" features either the Stargate franchise's first gay kiss or first lesbian kiss, but not both. Laura Cadman, whose consciousness was trapped in the body of Rodney McKay, took control of his body and kissed both Katie Brown (for Rodney) and Carson Beckett (for herself).
- The Disembodied: A group of rogue Asurans (killer androids made of nanites related to the Replicators in SG-1) attempt to achieve ascension by destroying their original bodies and becoming incorporeal, but because they aren't organic this simply left them in a transient state.
- Distant Prologue: "Rising"
- Doctor Doctor Doctor: John Sheppard, Samantha Carter, Steven Caldwell and Abraham Ellis are all Colonels. Leads to a Funny Moment when all of them are put in the same room and greet each other.McKay: Seriously?
- Don't Make Me Destroy You: Otho gets Sheppard to hand over his weapons and agree to accompany him to the Tower by pleading that he think of his life and the lives of the surrounding civilians, many of whom would be killed if Sheppard tried to resist.
- Double Standard: Dr. Weir often chooses to take the moral high ground when it comes to how other cultures choose to save themselves from being destroyed by enemies that ravage and decimate entire worlds.
- Double Standard: Rape, Sci-Fi
- "Irresistible", where Lucius Lavin gets what he wants using pheromones — and has six wives as a result — is treated far too nicely by the team, and the episode itself is mostly a comedy.
- They only treat him nicely while they're under the effect of his pheromones. Once they're made immune to the effects, the protagonists give all of the villagers the same treatment so they can't be manipulated anymore and they send Lucius back to the village to be punished as they see fit.
- In "Duet", a female marine ends up sharing McKay's body by accident. After they argue a bit about who's in charge, she simply takes over after he falls asleep, takes his body for a run, then showers and sleeps naked. Later she wrests control from him to force him to kiss his girlfriend (which he'd been too shy to do), and then to kiss Dr. Beckett against the man's will. She did all this without ever asking McKay's permission, and while ignoring his protests. Again, it's a comedy episode and we're supposed to side with the woman during all of this.
- "Irresistible", where Lucius Lavin gets what he wants using pheromones — and has six wives as a result — is treated far too nicely by the team, and the episode itself is mostly a comedy.
- Dramatic Space Drifting: Two examples, both involving Asuran replicators (nanite robots).
- The first is after an Asuran scientist does a Heel–Face Turn. When the other replicators detect this they wirelessly reprogram him, causing him to attack the Atlantis team. They jetison him into outer space, with the episode closing on a shot of him floating around.
- The second is of Dr. Weir (now turned replicator) and her Ascension-seeking brethren floating in space after she tricked them into following her through the Stargate to protect the rest of the expedition.
- Dress-Coded for Your Convenience: Each side wears their respective military uniform, with a few off-worlders in native dress thrown in for variety. The good guys wear regular military clothes and the Wraith wear leather. And going the other way, the expedition's baggy battledress contrasts nicely with the Genii and their habit of Putting on the Reich.
- The jackets that expedition members wear also seem to have some correlation to their area of expertise; black for military (like Sheppard), yellow for medical (like Keller), blue for scientific (like Mckay), green for technicians (like Chuck) and red for operations/command (like Weir).
- Dude, Where's My Respect?? In Season 2 Elizabeth calls out John's superiors for treating him like this, when she discovers they're planning to replace him as military commander. Even though John, mere weeks after discovering the existence of the Stargate, successfully stepped up as second in command of a base in a different galaxy, managed a group of people he barely knew and fought off life-sucking aliens at every turn, all the military cared about was his low rank and past mistakes. Elizabeth fairly enough pointed out exactly how much he put his life on the line to protect Atlantis and it's people. (Helped by the fact that barely an episode before he'd been flying a suicide mission to save everyone under his command.) Even though Elizabeth secures John's position, the military still never approve of him.
- The Dutiful Son: Sheppard's brother in "Outcast", who stayed behind to take care of the family business while Sheppard was out on military ventures across the world after having a fallout with his father. They eventually manage to reconcile after their father's death.
- Dysfunction Junction: Atlantis is clearly an ancient, intergalactic dysfunction junction. Elizabeth is a Workaholic with virtually no life outside of the city, John has a horrible Guilt Complex, reckless abandon for his own life and a sociopathic, self-loathing dark side he tries to hide, Rodney is a self-absorbed egotist almost incapable of forming relationships, Teyla was orphaned from childhood and forced to lead her people at an improbably young age due to cullings from life-sucking aliens, and Ronon is a ruthless loner whose entire planet was wiped out and has spent the last seven years on the run with virtually no human contact.
- Early-Bird Cameo: SG-1's "Merlin" slips in an appearance before he is even alluded to on the mothership show.
- Early Installment Weirdness
- When the Genii were originally introduced they maintained a facade as primitive farmers in order to remain hidden from the Wraith, keeping up the charade even with regular trading partners and "friends." The facade was completely dropped by season two, where the Genii were known as a militaristic society to the galaxy at large, and had been for several decades. Possibly justified due to their acquisition of nuclear weapons at the end of the first season.
- The pilot has Teyla run off with a trailing afterglow and then reappear from Behind the Black, indicating some type of powers, only to never show up again.
- In the first season Wraith attacks coincided with people seeing strange ghost-like wisps. This is later dropped completely.
- Eating Optional: Played with for the Wraith. They don't eat food, they "feed" on lifeforce through a sucker on their hands. While it functions essentially the same, it is its own distinct process. Though one 'cultured' Wraith is shown to enjoy eating regular food, he admits that he just savors the taste but gains no sustenance from doing so.
- Embarrassing First Name: Meredith Rodney McKay
- Emotions vs. Stoicism: Sheppard and Weir. The dynamic was established in the first episode when a team was captured: Sheppard prepared to go in guns blazing, while Weir analyzed the situation. Their argument pretty much defined their differing personalities throughout the series:Weir: How do you know going off on some half-assed rescue mission isn't going to bring them all right back here to our doorstep?
Sheppard: Maybe it will... but it's the right thing to do. Why? Because it is!
- The Ending Changes Everything: Sheppard and Woolsey's plots in "Remnants" began to deconstruct a little more than halfway through the episode, but it is only in the final scene that we learn McKay's plot was also being manipulated by the A.I., and Zelenka was never actually in the episode at all.
- Enemy Mine: "Common Ground", the introductory episode of Todd the Wraith, features him and Sheppard working together to escape a Genii base. This would lay the foundation for later episodes, where Todd would collaborate with Atlantis against both Michael and the Replicators.
- Engineered Heroics: Lucius Lavin goes into the Engineered Heroics business after his Mind Control empire falls through. Then he tries to haggle on the payment after the hired villains did their part... When the protagonists show up, the hired villains, as their sworn enemies, perform some actual villainy.
- Establishing Character Moment
- Before you knew his name, you only knew Sheppard as the one to save Jack O'Neill's life from a wayward Ancient attack drone. He gets another one half an episode later when some of Atlantis's people are captured and he immediately launches a rescue mission despite all logical protests.
- Ronon's introductory episode has him getting into a fistfight with Ford (who is inhumanly strong and crazy because of a Psycho Serum accident) and not only matching him in combat, but seeming to have the edge.
- Colonel Ellis, commander of the Apollo, clashes with the Atlantis expedition personnel over how to deal with the Replicators and dismisses McKay's technical abilities as a potential weapon, highlighting how he is less cooperative and used to the Pegasus galaxy than Colonel Caldwell.
- Everything's Better with Spinning: Subverted: The symbol ring on the Pegasus gates are stationary and the illuminated panels simply give the illusion of spinning.
- This makes the line, "Spinning is so much cooler than not spinning!" from SG-1's 200th episode even funnier, since "200" aired a few years after Atlantis started and the line is probably a light-hearted jab at Atlantis.
- Evil Has a Bad Sense of Humor: Todd as a people-eating space vampire has a quite morbid sense of humor. He arranges an alliance with the humans by offering to shake hands (from which Wraith feed on people) before noting that he was joking and commments on some fruit he prepared for a later meeting with "I hope they prove as delicious as the farmers who grew them".
- Evil Is Visceral: The Wraith use Organic Technology and are not very pretty themselves.
- The Evil Prince: Subverted in an episode where Atlantis visits a royal family who possess the gene required to operate Ancient technology necessary to protect their planet from the Wraith. The king's son is a snobbish aristocrat who is clearly plotting to overthrow his increasingly fragile father and lock up his sister in the process. The subversion comes when it turns out that it was the (apparently well-intentioned) Evil Chancellor who was the real brains behind the plot and locks up the ambitious prince when he has no more use for him.
- Expendable Alternate Universe:
- Subverted in "McKay and Mrs Miller"; the techies have no qualms doing great damage to an alternate reality until they find out that life also exists in it (a chance that was considered astronomically small).
- The penultimate episode, "Vegas", is set in a separate alternate universe where Sheppard is a CSI-style detective in Las Vegas hunting down a rogue Wraith that somehow got to Earth. However, before the Wraith dies, it transmits a signal throughout the Multiverse shouting Earth's location. The Alternate!Woolsey's response to this is that it's pointless to worry about saving every possible universe and is sufficiently pleased to have prevented the invasion in his own. Unfortunately for the primary versions of the cast, the message makes it to their universe, setting up the finale.
- Face Death with Dignity: Colonel Marshall Sumner, USMC, calmly follows the Wraith sent to collect him from his cell, and faces the Wraith Queen without showing fear or asking for mercy. The Queen herself notes that she has not tasted such valor in many years.
- Face–Heel Turn: Otho towards the conclusion of "The Tower".
- Fakeout Escape: Sheppard uses this in "Aurora" to escape from a virtual-reality cell.
- Family Versus Career:
- Played straight in season three, where we meet Jeannie Miller, Rodney McKay's sister. She had left a promising career in theoretical physics to raise her daughter, much to her brother's consternation. Jeannie makes it clear that she chose to be a wife and mother and is happy with her decision. But despite being a Housewife, she's still a Hot Scientist (and even occasional Action Girl) who solved a problem that had baffled McKay for years "in [her] free time, with fingerpaints."
- Subverted in season five when Teyla struggles to decide if she should rejoin Sheppard's team after her pregnancy and risk leaving her son without a mother, or if she should give up fighting for the freedom of the galaxy which is also very important to her. In true Action Girl fashion, she does both (it certainly helps to have a House Husband in these sorts of situations.)
- Famous Last Words: When Peter Grodin stays behind to bring the Ancient Satellite Weapon online, he laments that his only regret is that he was unable to get enough power to fire off a second volley and take down another Wraith Hiveship;Dr. Peter Grodin: I'm sorry.
- Fanservice: McKay conjures up an image of Col. Carter to act as a conversation/idea foil for himself as he tries to figure a way out of a sinking Puddle Jumper. At one point he imagines her in nothing but a skimpy blue bra. Yes, Rodney creates his own fanservice and the audience gets to observe for free. In the episode commentary, Amanda Tapping says she thinks she looks like "a lady who just had a baby" (i.e., out of shape). Martin Wood (the director) and David Hewlett both drown her out with assurances that she's plenty good-looking.
- Faux Action Girl: Laren in "Travellers" beats Sheppard up while he's her captive and gives the air of a confident captain who knows what she's doing, but she's absolutely useless in a real fight, can barely use her own ship, is constantly at the mercy of the Wraith, and does nothing helpful at all in the entire episode, merely hindering Sheppard while he saves the day. Furthermore, her day-to-day fighting gear includes ridiculously high heels that she can barely run in. The only thing she's good for is gratuitous fanservice and Ship Tease with Sheppard.
- Feed the Mole: Played for Laughs. When Sheppard realizes that the girl sent he "rescued" was a wrather worshipper plant, he tells her that on Earth, they are fighting a war against an powerful and evil enemy, clowns.Sheppard: They just keep sending them in.
- Flip Personality: When Cadman is trapped in McKay's body in "Duet", they act like this.
- Floating Continent: Atlantis is both a floating city and a spaceship; in the original mythology described by Plato, it was a large island/small continent on Earth.
- Food and Animal Attraction: Sheppard discovers a planet inhabited by glowing dots that are attracted to his power-bars. Since they also register strongly on Lantean life-signs detectors, he ends up exploiting this to kill a Wraith: he attracts a bunch of the creatures, sticks a power-bar on the wraith, and then radios the puddle-jumper sent to rescue him, telling them to shoot at the strongest life sign they see.
- Force-Field Door: Though Atlantis is at least sensible enough to have physical bars with the forcefields between them.
- Foreign-Language Tirade
- Zelenka is known to rant in Czech when frustrated.
- Hermiod frequently complains about humanity in Asgard, which is actually just English in reverse.
- Forgotten Phlebotinum: Much is made of the need for Zero Point Modules for high-power tasks (to power the city's shields and drones, and to dial Earth). No one seems to remember that way back in SG-1 Season 2, O'Neill built a single-use power supply capable of dialing eight-chevron addresses. Not long after, Carter even is able to build a new one. At no point does the expedition consider using this device as a replacement for a ZPM.
- Galactic Conqueror:
- The Wraith in the Pegasus Galaxy, although they don't so much rule as they do feed. Also, the Wraith do a lot of fighting amongst themselves, on account of there not being enough food to go around. Thus, no one person (or hive queen) actually controls their galaxy.
- The former Wraith named "Michael" became such a threat in his own right in the later seasons. After he started his Hybrid project he started lusting after power for its own sake. His end goal became to supplant both humans and Wraith with his Hybrid minions by annihilating everything else.
- Geeky Turn-On: Dr. Weir distracts a scientist by talking about World of Warcraft in "The Return, Part 1". Incompetently.
- Gem Tissue: The crystals of planet M3X-387 may very possibly be this.
- Generational Magic Decline: The Atlantis expedition encounters one culture whose royal family have used Ancient technology to protect their people from the Wraith because they are the only ones who possess the ATA gene that is required to operate it (the main characters had the same problem when they started using Ancient tech, but they found a way to inject everyone with an artificial ATA gene). Despite efforts to strengthen the bloodline through careful breeding, their control is clearly diminishing. Sheppard is propositioned by the female heir to the throne specifically because his strong ATA gene will strengthen her child's claim over that of her brother's.
- Genre Savvy: Sheppard repeatedly show an awareness of sci-fi clichés and what roles they play, that Ronon is "Chewie" and Beckett is "McCoy". He also gets nervous when he's trapped in a room with pregnant Teyla during "Quarantine", noting that "every time one of these things happens in the movies, the pregnant woman goes into labor."
- Get Back to the Future: "Before I Sleep" exists at the nexus of this trope, Trapped in the Past, and The Slow Path.
- Get It Over With: The third-season episode "Common Ground", where the Wraith Todd is first introduced. After repeatedly feeding on Sheppard to the point that he has almost become a desiccated corpse, Sheppard intones him to do this. Then Todd gives back all the life-energy he took from him because he helped him escape from a Genii prison.Sheppard: Finish it.
Todd: As I told you, John Sheppard, there are many things about Wraith that you do not know.
- Getting Crap Past the Radar: Zelenka's Czech tirades are, by David Nykl's own admission, often more vulgar than anything the showrunners could get away with in English.
- Getting the Baby to Sleep: Teyla can only get her son to sleep by continually walking around Atlantis. Keller says that when she was a baby, she would only sleep in the car, so her parents had this habit of driving around the block at 3 AM.Teyla: Hmm... that would be lovely. At least I'd be sitting down.
- A God Am I: Played with. The Wraith do not openly claim to be gods, but they happily allow themselves to be worshipped as deity-like beings by their brainwashed human followers.
- Go-Karting with Bowser: Sheppard playing poker with a Wraith, though admittedly it was an alternate reality.
- Good Is Not Dumb: Col. Sheppard; Rodney McKay was quite surprised to find that Sheppard has a Mensa-worthy IQ.
- Not to mention most of the heroes from Earth have a bucketload of qualifications between them: Mckay (a phd in physics, another in mechanical engineering and one of the top scientists on earth), Zelenka (barely a step behind him), Elizabeth (2 phd's and a top UN negotiator before Atlantis) and Carson (top level medical doctor).
- Good News, Bad News:McKay: OK, I got bad news and I got good news.
Sheppard: What is it?
McKay: There's little or no chance of getting the DHD working — the system is completely out of wack. It's gonna take some incredibly intricate re-routing of the power in order—
Sheppard: Woh, woh! What's the good news?
McKay: That was the good news. The bad news is we lost life support.
- Grappling-Hook Pistol: When they are trapped in a collapsed mining facility, Carter, Keller and McKay try to climb out using a makeshift grappling hook. They joke about making a Grappling-Hook Pistol part of the standard mission gear for all off-world missions.
- Greater Need Than Mine
- After the control room of Atlantis is blown up in "First Strike", Col. Sheppard finds Ronon sitting on the ground with a large shard of glass sticking out of his shoulder. Sheppard asks him why none of the medics are attending to him, and Ronon says he would not let them because others in the room need help more. Sheppard immediately orders one of the medics to see to Ronon's injuries.
- McKay refuses medical assistance after he and Lorne are rescued from the wreckage of a collapsed building, insisting that they take care of Lorne first. Keller reacts by trying harder to help him since Rodney is a bit of a hypochondriac and would never pass up an opportunity for medical attention, but in this situation Lorne has a broken leg and Rodney is fine.
- Guile Hero: The Atlantis team.
- Gunship Rescue: "The Siege, Part 3" opens with the Daedalus emerging from hyperspace to save Atlantis from the Wraith assault.
- Hand Stomp: This is reversed in "The Prodigal" when hero Teyla shoves bad guy Michael off the top of the Atlantis main tower and then kicks his hands so he falls to his death. That's what you get for trying to steal a Mama Bear's baby.
- Harmful Healing: In "Mrs. Miller", Rodney McKay and his sister Jeannie are kidnapped by a wealthy industrialist to modify experimental nanoprobes so that they can cure his young daughter's cancer. The McKays reluctantly agree (not that they have much choice) and it seems to work successfully, until it turns out that the probes are far too aggressive and tried to fix a minor heart defect by stopping her heart to do maintenance, killing her, then reviving the girl... after several minutes of oxygen deprivation to her brain, rendering her a perfectly healthy vegetable.
- Hellbent For Leather: Increasingly so as the series went on. By season five virtually the entire main cast are wearing as their standard off-world outfits: black leather jackets (McKay, Keller, and occasionally Sheppard), black leather jacket and pants (Teyla), or black leather trenchcoats (Ronon). Then there's the Wraith...
- Hellish Pupils: The Wraith.
- Heroic Sacrifice
- Henry Wallace in "Miller's Crossing". We are shown the moments leading up to his decision to offer his life to the starving wraith, and then it cuts to his body being wheeled out in a bag.
- Griffin in "Grace Under Pressure", who defied McKay's order and forcibly sealed him in the rear compartment of the Jumper, knowing full well that this was a death sentence as the cockpit window was seconds from cracking and pouring in several-hundred cubic feet of ocean water.
- Hero of Another Story: Major Lorne
- Hero-Worshipper: Halling calls Teyla out on this in "Suspicion".Halling: [The Atlantis expedition] may reside here Teyla, but they are not the Ancestors. No matter how much you wish them to be!
- Hey, You!: When Woolsey is being reviewed and graded by the IOA he attempts to show how well he has settled in by addressing Atlantis personnel by their first names and referencing individual hobbies that they have. However, he accidentally calls Chuck "Chet" and, when Chuck corrects him, spends the rest of the episode referring to him as "you."Chuck: There is no Chet.
- Hidden Depths: Sheppard. He off-handedly mentions he passed the Mensa test, solved a brainteaser that even Rodney could not and one of the few items he took with him to Atlantis was a copy of War and Peace.
- Hidden Weapons: In "The Hive", when the heroes have been captured by the Wraith they need to activate a door panel located across the room from their prison cell. Ronon produces a dozen throwing knives after he's already been strip searched by the enemy.John: How many of those do you have?
Ronon: How many do you need?
- Hide Your Lesbians: Captain Alicia Vega, introduced in the premier episode of season five, was intended to be first canonically gay character in the Stargate verse. However, the only implication of this fact was a single scene at the end of the episode where, after unzipping her jacket, Vega invited Jennifer Keller to join her for a drink. This scene, and all of Vega's other scenes in the episode except for an exchange with Colonel Carter, was deleted from the episode before airing, and she was killed in her next appearance.
- Hive Caste System: The Wraith are divided into Queens at the highest strata (typically just one per Hiveship), followed by male Wraith (functioning in officer and science capacities), and Wraith soldiers at the bottom, who are under the constant mental influence of the higher groups. Sometimes there are human Wraith worshippers as well, who are akin to pets/slaves for the Wraith.
- Hollywood Encryption: Multiple times. Janus' lab pops up. He is meant to have his research encrypted with highly advanced encryption. It doesn't last long against the mind of The Smart Guy.
- Hollywood Giftwrap: McKay gives the pregnant Teyla a baby present wrapped this way: an iPod filled with recordings of his genius, so she can listen to them and make her son smarter in the womb.
- Hollywood Science: in Submersion, the underwater drilling platform has a moon pool giving access to the sea, implying that air pressure on the platform is equal to the sea pressure. However, the air pressure is normal, while the sea pressure is lethal. In reality, the moon pool would flood the platform.
- Well, it was built by the Ancients. . .
- Homeless Pigeon Person: Radek Zelenka reveals he's a major pigeon enthusiast and used to raise racing pigeons back on Earth.
- Honey Trap: In "The Lost Boys" and "The Hive" two-parter, during an infiltration of a Wraith Hiveship, Col. Sheppard rescues a cocooned girl, but he and his team are quickly captured by the Wraith and locked up again. She explains that she witnessed how her whole people were annihilated and cuddles up to him for warmth. Sheppard initially tries to comfort her, but when she gets suspiciously inquisitive about the world he comes from, he realizes that it's a ploy. It turns out that she's a Wraith worshipper and a personal pet of the Hive Queen.
- Horror Hunger: The Wraith, who can only feed on the live energy of humans or other Wraith.
- Hospital Hottie: Drs. Beckett and Keller
- Hostage Situation: John Sheppard, occasionally with other members of the Atlantis team, is frequently kidnapped and held hostage for resources, advanced technology or access to Atlantis. These dilemmas come up approximately once a season.
- Hot Scientist: Sam Carter
- Hunting the Most Dangerous Game: The Wraith occasionally capture humans and, instead of feeding on them, release them as "Runners". Runners have a tracking device planted within their bodies and are hunted from planet to planet. They do it both for fun and to use the Runners to find any isolated groups of humans that might be hiding from the Wraith but might help a Runner, not knowing what's on his trail.
- Hypocritical Humor
Jeannie: Good work, Radek.
- O'Neill cites Sheppard's record of having disobeyed orders, only to be immediately called on his own record of the same by Weir.
- From the episode "McKay and Mrs. Miller":
Zelenka: Thank you.
McKay: Yes, but try not to encourage him. He's got a bit of an ego.
- Hypocrisy Nod: the Geni, who attempt to justify their betrayal and attack of Atlantis by conveniently forgetting that they ambushed and tried to kill the people they had made an alliance with.
- I Am the Noun: In the first season, the captured Wraith the team dubs "Steve" is asked what his real name is, and he responds "I am your death. That is all you need to know."
- Idiot Ball: The writers literally could not think of a way to make the plot of "Midway" happen, so they recorded new dialogue for McKay that was inserted into the "Previously on..." opening with clips from "The Return" where he specifically mentions how they are not taking the standard precautions that they have taken on every other gate under SGC control.
- Having Sheppard, the person who has the highest Chair Interface ranking and one of two people who have used it against enemy fleets — i.e. has experience with something that we are told needs training and practice to use — fly a fighter X302 instead against a fleet of darts in "Enemy At The Gate" was a good idea because...? Ostensibly because he's the lead male role and so having other perfectly good fighter pilots out there anyway just slips the writers' minds. Not putting anyone in the chair at all so it could send out drones and defend itself added to the stupidity.
- I Have Boobs, You Must Obey!: McKay believes that the way to get a pair of ten year old boys to help them out of danger is for Carter to lift up her shirt, since that is how you get a male kid's attention. Carter points out that they can survive without resorting to that.
- "I Know You're in There Somewhere" Fight: Radek tries this with Ellia in "Instinct". It doesn't work.
- I Like Those Odds: Often stated by Ronon.Caldwell: I warn you, as a Goa'uld I possess the strength of many men.
Ronon: Then it'll be a fair fight.
- I'm a Doctor, Not a Placeholder: Carson often in season 1, specifically in "The Brotherhood".Carson: For the last time, I'm a doctor, not a bloody fighter pilot!
Carson: I'm a bloody medical doctor, not a magician!
- Immune to Bullets
- The Wraith (at first, before Lowered Monster Difficulty set in). Later seasons handwave the Wraiths increased vulnerability to bullets by explaining that their healing ability is directly proportional to how recently they have fed. something suggested as early as the first episode; with more Wraith awake and less food to go around, a running subplot throughout the series, they begin to lose their advantage.
- The Asurans.
- Impaled Palm: In "The Defiant One", Major Sheppard has to attack an especially persistent Wraith with a knife after they've run out of ammunition. Being able to regenerate, the Wraith just takes advantage of being stabbed in the palm to disarm him.
- Imperial Stormtrooper Marksmanship Academy: Averted, the Wraith frequently manage to shoot Atlantis personnel, including the stars of the show, but since they only use stunners the cast can keep coming back for more.
- Imperiled in Pregnancy:
- As Teyla neared the end of her pregnancy, Michael kidnapped her to use her son as a testbed for his human-wraith hybrids. One Alternate Universe shows that had he finished his experiments, he would have created an army that would have effectively taken over the Pegasus Galaxy, but Teyla never saw it. In the proper time, the team manages to save Teyla and her baby.
- In another episode, Teyla is using her limited psychic skills gained from her Wraith DNA to temporarily mind control a particularely strong Wraith Queen, who are the psychic heavyweights of the vampiric race. Trapped in her own mind, the Queen wonders how Teyla is suddenly so strong that she could pose a challenge for her until she realizes that Teyla's unborn son is helping her, and the Queen nearly kills the child in return.
- Impossible Task Instantly Accomplished: McKay uses this as a Badass Boast.McKay: I'm Dr. Rodney McKay, alright? Difficult takes a few seconds; impossible, a few minutes.
- Improbable Age: Dr. Keller is named the head of Atlantis's medical team at the ripe old age of twenty-six. Supposedly because she was a Teen Genius.
- Inappropriately Close Comrades: Major/Colonel John Sheppard is professional enough not to engage in this (and besides that, the most Ship Teasing involving him were with Elizabeth (civilian) and Teyla (alien)), but there is a version of him who bucked the rules in the Alternate Reality Episode "Vegas". When Sheppard was stationed in Afghanistan, he ignored direct orders to retreat so he could attempt a failed rescue mission that got him discharged from the air force. The alternate universe version of Rodney McKay figures out that it was because Sheppard was in a relationship with one of the soldiers he tried to rescue, which he doesn't deny.
- I Never Told You My Name: In the episode "Common Ground", Sheppard is captured by Kolya, who allows a captive Wraith to repeatedly feed on him. When Sheppard is thrown back in his cell, the old man in the next cell tries to make some idle chat until Sheppard realizes that he never introduced himself. The "man" admits that he heard his name when he fed on Sheppard.
- Infinite Supplies: Throughout the first season the expedition refers to the problems that will arise when their supplies run low due to their isolation from Earth, but they never actually run into a problem. Possibly justified in that they are out of contact for only about eight months, and likely brought more than enough for at least a year, supplemented by trades for food with various human societies.
- Inflationary Dialogue
Sheppard: I got six, Teyla got...
- Sheppard's claims about how many Wraith he killed in "Sateda".
Sheppard: I got nine, Teyla got eight, Ronon got the rest.
Sheppard: Only killed eleven, twelve Wraith.
- Innocent Innuendo: This exchange from episode 5.15, as Richard Woolsey sees that a women he has been flirting with found his balcony hang-out spot:
- Instant Expert: Sheppard when it comes to Ancient Technology. He was even recruited after accidentally sitting in the Ancient Control Platform in Antartica, managing not only to activate it but demonstrate an exceptional level of control, despite having no idea what he was doing!
- Instant Sedation: When Sheppard, McKay and an Atlantis assault team are gassed by the Genii, they all collapse immediately but suffer no long-term effects.
- Insufferable Genius
- The expedition's science teams are an army of Insufferable Geniuses, with Rodney McKay as their supreme leader. The two exceptions are Carson Beckett and Radek Zelenka, who are just as smart as the rest, but are rather humble about it.
- Inverted in Rod McKay's reality, where Rodney is humble, but their version of Sheppard is constantly showing off his intelligence.
- Interdimensional Travel Device: In "The Daedalus Variations", an alternate McKay builds an "alternate reality drive" which has this function. The only problem is, it does not have an off switch or any way to control which reality it jumps into. This leads to one universe's worth of main characters being stranded in the wrong reality and another universe's worth dying of starvation before they can figure it out, before the actual main characters bootstrap on their research and discover a way to make it backtrack through the realities it came from (so they can at least get home, if not actually exploit the drive).
- Interrogating the Dead: In the series finale "Enemy at the Gate", the Wraith leader of the Hiveship attacking Earth revives the fallen Ronan so he can question him about the infiltrators on his ship. This gives his friends the opportunity to rescue him.
- Ironic Echo: When Ronon refuses Teal'c's help in learning to handle the I.O.A. he insists that he knows "how to play the game." In response, Teal'c accuses Ronon of causing the attack on Sateda and Ronon draws his gun in anger calling Teal'c a liar. Teal'c calmly comments that yes, he was lying, but Ronon would never dream of doing such a thing in his upcoming I.O.A. meeting since he does, of course, know "how to play the game."
- Jerkass: Kavanagh, described by the producers as the most irritating person in three galaxies.Hermiod: Doctor Kavanagh?
Hermiod: Stop... talking... please...
- Jerkass Has a Point: Not one specific point, but a general mentality. When Teyla finally has enough of Sergeant Bates' insinuations that she is either a willing traitor or unwilling information leak, Sheppard points out that Bates is the head of base security and it is his job to look for potential threats.
- Bates actually had a specific point. He thought it wasn't a coincidence that the Wraith kept showing up on offworld missions when Teyla was present. It turned out that her necklace was a tracker Sheppard inadvertantly activated. He was wrong about her loyalty, but he was right that all those close calls happened because she was present.
- The Judges in the clip show episode may come off as ungrateful bastards, but they're not entirely wrong when they accuse the Atlantis crew of being responsible for a lot of the sector's troubles. Having broken quite a bit despite their best efforts and good intentions.
- Jerk with a Heart of Gold
- Rodney, oh so much Rodney.
- In "Tracker", when Keller has been kidnapped by a Runner in order to treat the young girl in his care, the child explains that he is not really mean, he just acts that way. Keller comments that she knows someone just the same, but the nature of the episode means that she could be talking about Rodney or Ronon.
- The Juggernaut: The Super-Hive in the Grand Finale. Specifically, it's massive, and thanks to being powered by a ZPM, its Healing Factor (Wraith shielding systems are generally fairly nominal, going in for healing abilities instead) is insanely powerful.
- Juggling Loaded Guns: Pretty much every time Rodney McKay fires a gun. Justified since he has no military experience and no training with firearms. In one episode, he frantically asks someone else what the hell he is supposed to do when his gun runs out of bullets. His best part was when he tried to shoot a Wraith, and hit the magazine release instead.
- On the other hand, on one occasion, he juggles himself by accurately shooting and killing a Wraith while hopping on one foot.
- Just a Machine: Stargate Atlantis and its parent show Stargate SG-1 feature this trope heavily in episodes where characters interact with A.I.s, up to and including causing the slow deaths of non-hostile Asurans out of paranoia. The only difference is that Stargate SG-1 relatively paddles in the shallow water compared to the depths of amorality the Atlantis Team sink to. The Atlantis team generally don't even question the morality of their actions or the value of a sentient A.I consciousness, and have even patted themselves on the back for what they've done. The most they've ever shown is the slightest twinge of remorse after Dr Weir sacrificed herself and even that was never brought up again, dwelt on, or their actions seriously questioned.
Carter: Does she know why she was created?
- This attitude is at least challenged once when Rodney realizes that in order to destroy the Asurans he has to build one and send it to its "death", and this was a low-level sentience.
McKay: Of course.
Carter: Well, then, she has a certain amount of self-awareness.
McKay: Yeah, so?
Carter: "So"?! Honestly, I'm not sure how comfortable I am sending her to her death.
McKay: "Death"? It can't die — it's not alive! It's a programme!
Fran: I quite look forward to it.
- Fran eventually even made McKay uncomfortable with her blase attitude towards (and excitement for) her impending destruction.
McKay: You do?
Fran: One always wishes to fulfil one's purpose.
McKay: Well, I just ... I just imagined you'd rather keep being than, uh... uh, than not.
Fran: Certainly you're not worried for me, are you, Doctor?
McKay: No, no, that would be silly.
Fran: (smiling at him) Yes, it would.
(Rodney turns away and walks over to Radek)
McKay: Should never have given it speech.
- Kangaroo Court: The trial in "Inquisition". They arguably could have convicted Atlantis fairly on the charges, but instead they had one war survivor looking for a scapegoat and another judge being bribed by the Genii to vote guilty. The lead judge is actually open to being persuaded either way by a good argument. The war survivor was so biased she was going to vote guilty no matter what, but they manage to win the trial by convincing the reasonable one and giving the corrupt judge a sufficiently juicy counter-bribe to vote in their favour.
- Kind Restraints: Sheppard is confined to his room while turning into the Iratus bug; he asked for it, he warned everyone, yet no-one seemed to take him seriously.
- Kingpin in His Gym: When we are first introduced to Commander Kolya of the Genii, he is having a sparring session with some of his military subordinates before he's interrupted for a new mission.
- Kissing Under the Influence
- In "Duet", McKay has the consciousness of Laura Cadman, a Marine, trapped within his mind. She was able to take control of his body for brief moments, longer if he was sleeping or voluntarily surrendered control, and she twice took the opportunity to kiss other members of the Atlantis expedition. First she kissed Katie Brown, a botanist with whom Rodney had a date, and then she kissed Carson Beckett right before the dangerous experiment that would either restore her to her own body, or kill her and Rodney both.
- When Sheppard was infected by Beckett's prototype Wraith retrovirus he kissed Teyla when he began to lose his self-control.
- While possessed by ancient warrior entities, Phebus (Elizabeth) kisses Thalen (Sheppard) in order to convince the other Atlantis personnel present that they were husband and wife.
- Kneel Before Zod: Wraith queens have mind control (and Power Echoes) at their disposal and could force captives to do just about anything. What do they want them to do? KNEEL. Sheppard tried to put his own spin on this at one point; the Wraith were not pleased....
- Last-Name Basis: McKay frequently addresses Sheppard by his military rank as a form of respect.
- Last of His Kind: Ronon initally assumed he was the last of the Satedans. "Reunion" reveals that 300 Satedans survived in shelters outside of the city and migrated to other world such as Belkan and Manaria when they realised that their was nothing left to rebuild.Solen Sincha: Drink and rejoice Ronon! You are not alone!
- Left It In: In "Letters from Pegasus", McKay gives a videotaped message to Ford, who is editing a bunch of these messages together to send back to Earth. McKay recorded the message while severely sleep-deprived, so it is full of rambling, back-tracking, and McKay telling Ford to edit out the last thing he just said.
- Less Embarrassing Term
- Rodney insists that he did not faint, but "passed out from manly hunger."
- In another episode, he started to say that he was "escaping," but quickly changed it to "effecting a strategic retreat". Likely homaging Dr. Smith from Lost in Space, who said the same thing.
- Life Drinker: All the Wraith, who drain the life from their victims and have no natural lifespan if they are well-fed. The process is referred to as "feeding" and the victim visibly ages during it; those who are fed on until death become mummified husks. The Wraith refer to the effect on the victim as "taking years" from the victim, although Beckett explains that the aging process is actually due to a complex chemical interaction that humans do not completely understand.
- Littlest Cancer Patient: Sharon from "Miller's Crossing". She does not make it.
- Lotus-Eater Machine: In the episode "Home", the characters think they've found a way to return to Earth, though it doesn't become apparent until about midway through the episode that their Lotus Eater Machine is individual and doesn't include the others. Each of their worlds was designed with everything they wanted to keep them from fighting back, but starts defying logic in ways that provoke their suspicion. Major Sheppard somehow figured this out early, and to test it, included in his mental fantasy a sweet apartment he had never seen, an attractive girl that he remembers (unsuccessfully) asking out, and two of his deceased friends showing up without explanation.
- Love Triangle: At the end of season four and the beginning of season five, Ronon and Rodney both begin to have feelings for Keller, and in "Tracker" they admit their feelings to each other and agree to allow Keller to make the decision. She ultimately chooses Rodney, but a deleted scene in "Trio" (lightly) implies that it was because Ronon took too long to make a move after their first spark in "Quarantine". Once Ronon realizes this in "The Lost Tribe" he calmly accepts the choice and stops his pursuit.
- Lowered Monster Difficulty
- The Wraith were first introduced as the ultimate evil in the universe. They were the race that killed the Ancients, and the Atlantis team spent much of the first few seasons running and hiding from them. They were practically Immune to Bullets due to their rapid Healing Factor, requiring huge amounts of firepower to bring down, and just two of their Hive Ships posed enough of a threat to Atlantis to warrant the team trying to blow the place up themselves, rather than let them get their hands on it. After a couple seasons, however, they die just as easily from a burst of P90 fire as any other enemy Mook, although they sometimes can eat a few pistol rounds and keep coming, and their ships tend to go down even easier. By the series finale, Sheppard is casually mocking most of the Wraith he comes into contact with.
- Justified for a couple of reasons. First, the Expedition mostly knows about the Wraith from the residents of Pegasus, to whom they are an omnipotent evil, and from Ancient records, when the Wraith were at the very height of their power, and aren't particularly well informed as to their capabilities. Second, the Wraith are stronger and heal better depending on how recently they've fed and their level in the caste system. At the beginning of season 1 all the Wraith are awakened and basically go on a feeding spree, culling huge amounts of planets, and even then they are literally desperate to get to Atlantis so they can get to Earth with its 6-7 billion population because there isn't enough to go around. By season 5 they are significantly weakened and starving, while the Expedition and SGC forces in general have figured out how most effectively to fight them, with the latter having upgraded their ships with extremely powerful Asgard weaponry. Not the first army in history to get defeated by starvation, right?
- The first attack by the Mist Monsters in "Whispers" manages to grab Captain Vega in total silence, without being seen by the other people present even though they were looking at her at the time, and kill her in the few seconds before the other team members catch up. The Monsters never manage to kill another Atlantis member in the rest of the episode.
- The Wraith were first introduced as the ultimate evil in the universe. They were the race that killed the Ancients, and the Atlantis team spent much of the first few seasons running and hiding from them. They were practically Immune to Bullets due to their rapid Healing Factor, requiring huge amounts of firepower to bring down, and just two of their Hive Ships posed enough of a threat to Atlantis to warrant the team trying to blow the place up themselves, rather than let them get their hands on it. After a couple seasons, however, they die just as easily from a burst of P90 fire as any other enemy Mook, although they sometimes can eat a few pistol rounds and keep coming, and their ships tend to go down even easier. By the series finale, Sheppard is casually mocking most of the Wraith he comes into contact with.
- MacGuffin Super Person: Teyla's baby is a MacGuffin for Michael as he wants to use the newborn's DNA to advance his hybrid research. Since Teyla's an Action Mom, he doesn't get very far.
- Mad Artist: In the Alternate Reality Episode "Vegas", Todd the Wraith (a race of vampiric human-insect hybrids) is captured after his Hiveship was destroyed in a failed invasion of Earth and held in Area 51. He eventually goes delirium from starvation and starts reciting Wraith poetry.Todd: Fish in a pond, busy busy, lots to do, here and there. Dry as a desert outside, no place to go. Eat up, get stronger, think and hope, think and hope. Don't look now! Oh, keep dreaming. There must be some other reason for your existence. Defiance tastes like life itself. No river. No water. Dry as a desert. Darkness all around. The harvest moon is rising. Wraith are never-ending. I know the future. Come inside. I'll show you your destiny... John Sheppard.
- Mama Bear: Teyla. Threaten her child, get thrown off a skyscraper.
- Weir is this for pretty much the entirety of the Expedition.
- Manic Pixie Dream Girl: Richard Woolsey, perennial stuffed-shirt bureaucrat, meets a beautiful scientist aboard Atlantis who persuades him to go to movie night and come out of his shell. Too bad she is a mental projection from an A.I. that was created after gleaning his romantic and sexual desires from his mind.
- Married to the Job: Sheppard and his ex-wife Nancy divorced due to the inherent danger of his job; she dreaded the inevitable phone call that Sheppard would not make it home. Interestingly enough, said ex-wife fell into this trope with her new boyfriend due to the nature of her job at Homeland Security. She even tells Sheppard that she now understands what it's like.
- Sheppard and Weir are both like during the show as well, they're both far too dedicated to Atlantis to even consider potential relationships most of the time and gradually lose interest in their old lives back on Earth. (When Sheppard actually takes a rare vacation he doesn't even bother leaving the Pegasus galaxy and Weir refuses to take a break or go on a date on Atlantis's general day off and goes into Heroic B.S.O.D. when they're forced to leave Atlantis in Season 3).
- Mauve Shirt
- Dr. Peter Grodin was a science officer introduced in "Rising" that served as Elizabeth Weir's assistant and primary control room technician during the first season. Craig Veroni had previously appeared in the episode "Grace" of Stargate SG-1, but it was never confirmed if it was the same character or the same actor playing two different people.
- Sergeant Bates is appointed by Dr. Weir as head of Atlantis security, and spends much of season one butting heads with Major Sheppard over how to treat the Athosians as a potential security risk.
- Chuck the Technician was a nameless character for the first three seasons until Torri Higginson accidentally called him by the actor's first name and that was kept in the show. He recurred until the finale as one of Atlantis's operators and technicians.
- Amelia Banks was a recurring technician introduced in the fourth season; in the fifth season she was given personal hobbies and a minor relationship with Ronon.
- Meaningful Echo: When Colonel Dillon Everett was sent to Atlantis to oversee the city's defense he clashed with Dr. Weir, and when he eventually commended her on her negotiations with the Genii she wryly remarked that "Maybe there's hope for me yet." Several episodes later, when Dr. Weir congratulates Colonel Steven Caldwell, the commander of the Daedalus that she had repeatedly clashed with, on his own performance, he also remarks that "maybe there is hope for me yet."
- Meaningful Name: Ronon is phonetically similar to ronin, the Japanese word for a Samurai warrior without a master, Ronon's situation when the expedition first encountered him.
- Medieval Stasis: Justified, as the Wraith destroy any civilization which is advanced enough to pose a threat.
- Another episode had a society that got advice from an Ancient computer terminal, when the Ancients left the galaxy, the people stalled in their development and refused to build anything more than what they were instructed to.
- Mental Story: In "Home", the main characters apparently manage to return to Earth, but it is actually an illusion of Earth fabricated from the memories in their heads.
- Mercy Kill: Sheppard kills Colonel Sumner after he had been fed upon by the Wraith. When Colonel Dillon Everett, a friend of Sumner's, arrives on Atlantis, he wonders just what made Sheppard feel that, after only knowing Sumner for a few days, he was qualified to make that call. When Everett himself is fed on by a Wraith he tells Sheppard that he made the right call, and wishes that Sheppard had been there for him.
- Mike Nelson, Destroyer of Worlds: Rodney McKay and his talents of obliterating planets, solar systems, alternate universes....
- Mile-High Club: McKay and Keller were implied to have joined at the end of "Brain Storm".
- Mistreatment-Induced Betrayal: a rare version where it's the heroes doing the mistreating. Because of how little the Atlantis expedition values non-human life, more than once characters who trust Atlantis to help them or give them sanctuary after they helped them have found themselves vastly disappointed. Michael is, of course, the big example here — it's specifically stated that if the Atlantis people had allowed him to find a home in Atlantis and hadn't betrayed him, he would have been their ally (and millions of humans would probably not have died in his crusade against both Wraith and humans for not accepting him).
- Dr. Weir is an odd inversion, she was treated horribly by Atlantis when she came back as a replicator and then she helped them destroy the peaceful replicators who depended on her.
- And Todd is an odd subversion. He is treated badly as a prisoner for months when he comes to Atlantis proposing a truce and sacrificing his own hive ship and Queen for their defence against other Wraith, and yet he still trusts them — although when the Antaross device is activated he assumes it was Atlantis considering their track record. But being the Manipulative Bastard he is, Todd is good at turning a bad situation to his advantage anyway.
- Monster Clown
- Mentioned half-jokingly by Sheppard when one of the natives asks him if he is afraid of the Wraith. He says no, what he is really afraid of is clowns, eventually adding he is at war with them. They try to fight them off, he says, but there are hundreds of them, pouring out of Volkswagens.
- Brought out for real when Rodney McKay and Sheppard are being attacked by an entity that feeds on their worst nightmares: rowing a boat through a stormy whale-infested sea... with a clown sitting behind them.
- Monstrous Cannibalism: The vampiric Wraith are shown to not be averse to feeding on members of their own species. This practice increased significantly during the Wraith Civil War, since there were not enough humans to go around (the Wraith having been woken up early from their hibernation).
- Moral Dissonance: Too much to list here. Lampshaded occasionally... ONLY occasionally.
- Mr. Fanservice: Colonel Sheppard; Ronon Dex
- Ms. Fanservice: Teyla's workout outfit is pretty much designed to make her this, even though the majority of her fanbase is female. At one point during the filming of a fight scene the director had Rachel Luttrell reposition herself to more prominently display her body to the camera.
- Multinational Team: You can have fun spotting the flags on the base uniforms.
- Multistage Teleport: Justified; using a Stargate to go directly between galaxies requires the use of a Zero Point Module, a limited-availability technology that is often required elsewhere (for instance, powering the Ancient Control Chair that defends Earth), so a more practical method is required. Cue the McKay/Carter Intergalactic Gate Bridge. Instead of a single Stargate trip requiring an impractical amount of power, the journey is made through thirty-four daisy-chained Stargate trips, each one relying on an ordinary Stargate battery. The traveler doesn't even feel the difference; travel time is reduced to about thirty minutes, compared to traveling on Faster-Than-Light ships, which can take weeks.
- Multitasked Conversation: When Woolsey is seeing the mental projection of an A.I. in "Remnants" he tries to hide it from the other Atlantis personnel since it would make him seem crazy. When he eventually winds up talking to real people and the A.I. at the same time he tries to pretend that his (almost panicked) dialogue with the A.I. is meant for the real person.
- My Greatest Failure
- Sheppard received a black mark on his service record, which was referenced as far back as the pilot, when he disobeyed orders in an attempt to rescue a downed pilot in Afghanistan. He did not make it.
- He gains two more during the show: failing to save Ford from going crazy under the Wraith enzyme and losing Elizabeth to the replicators.
- Ronon blames himself for bringing the Wraith to a village where he once spent the night when he was Runner.
- McKay destroyed 5/6 of a solar system when he let his hubris get the better of his judgement. Since it was uninhabited, this is more of a Running Gag used to wind him up than a serious cause for angst.
- Sheppard received a black mark on his service record, which was referenced as far back as the pilot, when he disobeyed orders in an attempt to rescue a downed pilot in Afghanistan. He did not make it.
- My Significance Sense Is Tingling: Teyla has the ability to sense when Wraith are nearby. Turns out this is because a Wraith scientist added some Wraith DNA to one of her ancestors.
- My Sister Is Off-Limits!: When Sheppard meets McKay's sister, McKay's first words are to point out that she is married and she is his sister. When Sheppard gets defensive, McKay points out that he knows what Sheppard is like, "Kirk."
- Necro Cam: Parodied in the penultimate episode, a Shout-Out to CSI. The lighting, filter and camera effects that CSI uses are copied almost perfectly—except it's someone being murdered by a life-sucking alien.
- Neglectful Precursors: The Ancients and how. They accidentally created the Wraith, created the Asuran replicators, and for some reason, a device that creates tumours in your body that explode. After a few seasons many characters no longer regard them as the wisest of all species.
- Never Heard That One Before: When Zelenka tells Elizabeth that the Ancient computer system is incredibly redundant, Elizabeth repeats the "redundant" statement right back to him and he explains how that joke never gets old.
- Nice Job Breaking It, Hero!: The Atlantis team woke up the Wraith prematurely when they arrived, who have since then attempted to eat every living human in the galaxy and are all geared up to go and eat an entire new one thanks to information from, you guessed it, the Atlantis team.. They created Michael by acting with such cruelty and amorality towards him that you can't help but pity the Omnicidal Maniac, who in turn annihilates entire worlds of humans using the Hoffan drug that the Atlantis team helped develop three seasons earlier. They reprogrammed the Asurans to attack the Wraith (against their wishes)... who did so by attempting to wipe out all humans in the galaxy (their food). Finally, they gave the Lost Tribe the means to defeat the Wraith which — you guessed it — caused the deaths of so many humans by this point that the death toll is just ridiculous.. In other words, they are basically responsible for almost every recurring villain in the show.
- Nice to the Waiter: Woolsey attempts to show the I.O.A. that he has settled into his position as leader of Atlantis by demonstrating that he not only knows the first names of the technicians operating the city, but also their individual hobbies. This backfires when he accidentally calls Chuck "Chet" and later in the episode has to fall back on calling him "you".
- Not Even Human: the Atlantis expedition places a terrifyingly low value on non-human life. Despite the team willing to risk everything to save Dr. Weir when she was human, when she came back as a replicator they were entirely ready to not only shoot her in the back but invalidate her consciousness altogether. Never mind the ridiculous lengths they have gone to in order to Save the Villain when the villain is human — endangering the entire galaxy to do it — as soon as something is non-human and places even the slightest threat, the Atlantis expedition will react with lethal diligence.
- Not Helping Your Case: Carter asks Teal'c to travel to Atlantis in order to help tutor Ronon in how to properly deal with the I.O.A., who has a new member that is insisting on personal interviews with all aliens serving on SG teams. Ronon, however, insists that he does not need any such help, since he "knows how to play the game." So, Teal'c insults Ronon's Satedan history and drives Ronon to draw his gun; which of course he would never do, since he knows how to play the game.
- No Sense of Personal Space: Sheppard and Weir, which is particularly noticeable as they're normally in a professional setting. The fact Elizabeth has no problem with John sitting behind or even on her desk when they're discussing city matters is definitely unusual for a commander and her 2 in command.
- Not So Similar: Colonel Carter invites Teal'c to visit Atlantis and help Ronon learn to appease the oversight committee that has to approve his continued presence on the team. However, despite both of their status' as alien strongmen on a team of Earth humans, Ronon's emotional nature and Teal'c's calm persoanlity immediately clash.
- Not That Kind of Doctor: McKay
- The Nth Doctor: When Elizabeth Weir reappeared in the shows fifth season she was portrayed by Michelle Morgan, since her consciousness was in the body of a human-form Replicator. Before Atlantis began, Weir was portrayed by Jessica Steen in the SG-1 episode Lost City.
- Nuke 'em: In "Midway", once the military learns that there are Wraith within the SGC they plan to nuke the facility, despite the fact that other characters have pointed out that the Wraith cannot escape the facility and there are less a dozen enemy soldiers remaining.
- Oblivious to Love: McKay. In "The Brotherhood", "Inferno" and "Trio", he shows that he is completely unaware when a woman is actually interested in him until it is spelt out for him. Loudly.
- Oddly Small Organization: It seems that The Atlantis Expedition originally only had two commissioned officers assigned to its security forces, Marshall Sumner (Colonel, USMC) and Aiden Ford (Lieutenant, USMC). The last-minute inclusion of John Sheppard (Major, USAF) brought that total to three, which seems extremely low for an expedition whose personnel number in the hundreds until you realise the bulk of the personnel are civilian scientists and there are only a couple of dozen military members on security detail.
- Of Corsets Sexy: Women of many of the societies in the Pegasus galaxy wear laced bodices as part of their everyday wardrobe.
- Older Than They Look: Sheppard tries to get Ronon to heed Teal'c's advice on dealing with the I.O.A., pointing out that he has to know something since he is something like a hundred years old. Teal'c is 159 years old during the airing of "Midway".
- Ominous Crack: This has happened to McKay twice, probably because his Oh, Crap! expression is so funny.
- In "Grace Under Pressure", Rodney and Lieutenant Red Shirt crash a puddle-jumper into the ocean on a test flight. They look out at the water in wonder and then — surprise! — Ominous Crack. Redshirt manages to push Rodney into the other section of the jumper before the cabin floods.
- In "The Ark", Rodney is stuck somewhere in the space station looking out at space. He starts panicking when he spots a piece of equipment hurtling toward the glass from outside. It hits... and nothing happens. Rodney's relief quickly turns into terror as the glass starts to crack. He only just gets into his space suit in time.
- Once More, with Clarity!: At the end "Be All My Sins Remember'd", there's a noticeable delay between the fleet's escape to hyperspace and a Wraith Hive's own escape jump. The teaser for the following episode, "Spoils of War", opens with a reprise of the ending. We discover that the delay was because Todd was waiting for Dart pilots to make it back to the ship with recovered Zero Point Modules.
- One-Man Army: Ronon in "Sateda", where he single-handedly takes down multiple Wraith platoons in the ruins of his homeworld.
- Only Known by Their Nickname
- It's not entirely certain whether the Wraith even have names. They certainly don't use them around humans, who wind up calling recurring Wraiths things like "Michael", "Todd", and "Kenny". Strangely, the Wraith sometimes use the human-bestowed names in each other's presence as well.
- Puddle Jumpers. After Sheppard christened it in the pilot, (in reference to a light aircraft and the event horizon of the Stargate), everyone refers to them by that name. The Ancients actually referred to them as "Gate-Ships".
- Orbital Bombardment: Asuras. The Horizon. 'Nuff said.
- Organic Technology: The Wraith's.
- Other Me Annoys Me: In one episode, an alternate universe version of Rodney McKay appears. This version is charming, extraverted and socially skilled. The regular Rodney ends up disliking him because everyone seems to like him better. Once "Rod" is gone, though, everyone tells Rodney how annoying he was and that they're glad to be rid of him.
- Our Ancestors Are Superheroes: Not only does it have Ancient Astronauts, but they also sport non-technological superpowers, like telepathy.
- Teyla is revealed to be descended from humans who were experimented on by the Wraith, which gave them (and her, and others like her) the ability to sense the presence of Wraith. This ability also allows her to tap into the Wraith psychic network and even temporarily possess a Wraith. Of course, it works both ways.
- Our Vampires Are Different: The Wraith were once insects who evolved to a human-like state, but still retain their most basic instincts, which is to feed off of beings by sucking the life force (literally) out of your body with their hands, to rejuvenate their own life. Doing so renders them biologically immortal, some having been around for many thousands of years. It is unknown whether a Wraith can starve to death - though there is an instance where one wound up delirious and spoke in haikus. Feeding causes the target to age rapidly until they die; even partially fed victims die most of the time due to the levels of trauma involved. In fact, the human body would shut down far too fast for their liking, were it not for the special enzyme transferred into the victim that makes them somewhat more resistant to it. Said enzyme is produced by a set of glands in their forearms and can be used as a highly addictive combat drug for humans.
- It is said that the Wraith Healing Factor is dependent on when they fed last. A well-fed Wraith can knock humans through walls and swallow up to forty bullets before dying — as Sheppard puts it, "I can see you just fed which means your regenerative powers are at their highest... but I seriously doubt you can grow a new head". However, their physiology is similar enough to humans that Wraith weapons designed to stun humans work on their owners as well. Additionally, a retrovirus can suppress the insect DNA, transforming the Wraith in question into a regular human with amnesia (temporarily unless a viral inhibitor dose is also used regularly).
- They're known to have a great weakness: a virus that makes a human not only immune to Wraith feeding, it also kills the offending Wraith. Plus, although they have a hive-like hierarchical society, they are quite willing to kill each other or resort to cannibalism if there's not enough food for all of them (as in the case of the show). In a sharp difference to vampires from other fiction, Wraiths can actually reverse the feeding process and transfer their own life force into someone else to heal them and restore their youth. They never do this lightly and reserve it to their closest worshippers and comrades only. Another weakness is revealed later: Wraith children are omnivores and can sustain themselves on any kinds of normal food but once they reach puberty, their digestive tract reverts to a dormant state. Hence the need for vampirism. In the final season, a modified version of the Wraith-to-human retrovirus is available to leave the subject as a Wraith but removes their feeding orifice, reactivating their digestive tract instead.
- The Expanded Universe reveals something that explains a great deal about the above, and why the Wraith hate the Ancients in the first place: they didn't actually evolve from the Iratus Bug, that was a polite fiction of the Ancients. They were originally humans experimented on by the Ancients, and not entirely willingly at that, being spliced with Iratus bug DNA as a potential method of becoming immortal if the whole Ascension thing didn't work out.
- Overt Rendezvous: Sheppard meets his ex-wife — who works for the Department of Homeland Security — on a park bench, in order to ask her to illegally dig up some classified information for him.
- Pardon My Klingon: Hermiod, the Asgard engineer aboard the Daedalus, expresses displeasure by cursing in his native tongue.
- Parody Episode: The episode "Vegas" starts out as a CSI parody episode, but rapidly gets serious until it hits a Bittersweet Ending.
- Parody Sue: One episode involves an alternate Rodney from another universe joining the main cast for a while, who has all of McKay's talents and none of his faults. Everyone seems to get along with him at first, but once he leaves the rest of the cast admits to being creeped out by him.
- The Password Is Always "Swordfish"
Sheppard: [typing and speaking] One six four three one eight seven nine one nine six eight four two.
- Subverted. In trying to access Dr. McKay's account to fix a computer error, Teyla laments about not knowing the password, and Sheppard responds with:
Sheppard: See? Doesn't take a genius.
Teyla: ... it doesn't?
Sheppard: 1643 is the year Isaac Newton was born; 1879, Einstein; 1968—
Teyla: The year Rodney was born.
Sheppard: NEVER underestimate the size of that man's ego.
Teyla: Wait, weren't there other numbers?
Sheppard: 42. The Ultimate Answer to the Great Question of Life, The Universe, and Everything.
- It has to be said he didn't guess it — he'd seen it before, and remembered it because he'd figured out what the numbers meant. The only reason McKay even typed the password in full view of Sheppard is because of his low opinion of military types as idiots, figuring Sheppard would never remember it. Which is odd, since he's known since the first season that Sheppard has a MENSA-level IQ.
Caldwell: We'll use my password.
- Also subverted earlier, when Rodney basically needs to hack into their own system.
Rodney: No, we'll use mine.
Caldwell: Why? Because you don't trust me?
Rodney: No, because it's a 26-digit alpha-numeric code that I may have to enter multiple times and I haven't gotten around to memorizing yours yet.
- Pay Evil unto Evil: the Atlantis team do this quite a lot here and there, doing some pretty bad things (sometimes even pretty terrible things) to people or creatures who are perceived by the team as evil or who have acted in aggressive enough ways to constitute a threat (with the Not Even Human point of view coming into play, non-human entities can get judged quite harshly). But the prime example has to be Michael's actions towards the Atlantis team after being betrayed and treated horribly a second time. This is how he justifies a lot of what he does... until he starts to lose his mind, anyway. Note that after the first time he was experimented on and mistreated horribly, he saved Atlantis, but apparently the second time was the charm (this may all have contributed to the aforementioned going crazy).
- Perfect Poison: Averted and played straight in "The Tower". The Lord Protector has been slowly poisoned over the past few months in order to hasten his death, but at the conclusion Otho dies almost instantly when he is cut by a poisoned knife.
- Perma-Stubble: Sheppard has a fluctuating level of stubble, but he is never fully without it.
- Pirate Girl: Larrin of the Travellers, while maybe not technically a pirate all the time, she sure acts like one in her first appearance.
- Platonic Life-Partners: Teyla's relationships with Ronon and Sheppard, while full of Ship Tease, has basically settled into this after becoming a mom. She even names her son after Sheppard and her father.
- Plot Tailored to the Party: Inverted in the episode "Quarantine" when everyone is locked in various rooms and each person has a part of the skills that they need to get out of the situation, except no one is in a situation where they can use those skills: McKay (The Smart Guy) does not have a computer, so Sheppard (The Hero) has to do all the technical stuff; Ronon (The Big Guy) is locked in an isolated room and is thus forced to do nothing; and Zelenka (another Smart Guy) has to do the dangerous air vent crawl that is pretty much Sheppard's trademark.
- Poor Communication Kills: Quite a few times, the team and the Atlantis expedition encounter naive and primitive cultures who worship or deify the 'Ancestors,' sometimes with their worship having serious consequences. Instead of explaining that the Ancients moved to the Milky Way and Ascended, and that they have a policy of non-interference in corporeal matters so strong that they would sacrifice an entire galaxy for their own enlightenment (although probably not in those words) they become suddenly mute or inarticulate when explaining could not only save the day but save lives. In one episode, "Brotherhood", the team lose a ZPM because the group on a particular planet believe they will be rewarded by the 'Ancestors' if they keep it and give it to them. Instead of explaining that not only did a bona fide Ancient give Alt!Elizabeth the address (which happened a couple of episodes prior) but that the Ancestors have already gone beyond this plane of existence, McKay pleads inarticulately that they need it with no elaboration or explanation to substantiate the fact that they aren't "stealing from the Ancients." Considering that Elizabeth Weir has specialized skills as a negotiator, this doesn't make much sense..
- Population Control: There's an episode where the team visits a world populated only by teenagers and children because every member of the tribe commits suicide at the age of 25. This is also because of an energy shield problem, one that was installed by the Ancients to protect the planet from the Wraith (the Big Bad of the show who are basically life-sucking space vampires)—only it doesn't cover the whole planet, so the Ancients gave their ancestors instructions on how to manage their population so they wouldn't have to leave the protected area. Atlantis eventually fixes the problem by providing the tribe with a greater power supply.
- Portal Slam: Like Stargate SG-1, a Stargate is open as long as the directors say, so it is not unusual for characters (or ships this time) to miss the wormhole. The Atlantis gate has a shield that obliterates anything that tries to appear from it, making a loud "FZZSSHH" sound as it does so.
- Power Creep, Power Seep: The Wraith's ability to regenerate varies on the episode. However, to the show's credit, they justified this by saying that their regeneration capacity was dependent on how recently and how much they had fed on life force, and that how resilient an individual Wraith is to physical damage, concurrent with the extent of their regeneration capacity, is also dependent on how old they are and consequently how many thousands of people they have fed on during their lifetime.
- Precedent Excuse: In the episode "Aurora" Sheppard is thrown in jail and tries to get the guard to let him out and take him to the ship's captain. The guard says he is under orders to make sure Sheppard speaks to no one. Sheppard retorts that the guard is already talking to him so the order is already broken, the guard then walks out wordlessly.
- Precision F-Strike: In the season five episode "Tracker", McKay clearly says "Holy Shit!" when a Wraith he thought he had escaped gets the drop on him, in contravention of Sci Fi Channel's censorship standards, to boot.
- Precocious Crush: Harmony spends most of her self-titled episode infatuated with Sheppard, even asking him to marry her before switching her affections to McKay at the end.
- Precursor Killers: The Wraith
- Precursor Worship: Downplayed from the previous series. But most Pegasus galaxy natives revere the Ancients as "The Ancestors".
- Pregnant Hostage: Teyla gets kidnapped while pregnant.
- Pre-Sacrifice Final Goodbye: In the last moments of the Season 1 finale Sheppard gets a moment with Elizabeth before his Heroic Sacrifice. They never actually get to say goodbye to each other but both realize his death is the only way to save their people and get to see each other one more time. Thankfully of course he survives and they get a reunion hug in the next episode.
- Product Placement: In "The Shrine", Sheppard and McKay drink Budweiser.
- Proud Warrior Race Guy
- From all indications, this was the reason why the Wraith wiped out the Satedans, and Ronon Dex continues their tradition on Atlantis. Each time the team hears tales of supposed super-soldiers killing many Wraith, Ronon remarks that they must be Satedans, and once was absolutely correct.
- During the fourth season, Teal'c, the Stargate-verse's original Proud Warrior Race Guy, visits the city.
- Psycho Serum: The Wraith enzyme confers strength, increased sensory ability and resistance to Wraith weapons at the cost of the user's sanity after a prolonged period of use, and harsher withdrawal symptoms.
- Puppeteer Parasite: In "Critical Mass", it is revealed that Colonel Caldwell has become host to a Goa'uld in the employ of one of the Stargate SG-1 villains.
- Putting on the Reich
- The Genii, although they become (relatively) friendly to Atlantis as the seasons go on.
- Downplayed in a season two episode that features a society which deports its prisoners to the vicinity of the planet's Stargate so the Wraith will feed only on them, where the Magistrate's uniform bears some fascistic overtones.
- Pyrrhic Victory: We learn that when the Ancients first fought the Wraith, they won every single battle, but lost the war through attrition, eventually abandoning Atlantis.
- Quip to Black: The second-to-last episode, "Vegas", was originally titled "CSI: Atlantis". It features an alternate universe where the cast is essentially transplanted into CSI, and "Detective John Sheppard" does a textbook one-liner at the end of The Teaser.
- Ragtag Bunch of Misfits: Despite early claims that the Atlantis expedition were Earths "best and brightest" it becomes pretty clear they're just the only ones crazy and screwed up enough to build a life in a different galaxy full of life-sucking aliens. The military commander is a dishonoured airforce pilot who the military pretty much kicked the curb for his disobedience, the head scientist so neurotic and pedantic no one on Earth will work with him, their native allies are horribly jaded from living their lives under the wraith and one spent 7 years alone on the run. The base commander is a bit more qualified but is still a previously-pacifist diplomat now trying to lead a war against life sucking aliens and even the medical doctor spends more time terrified of Atlantis than anything else.
- Ramming Always Works: The modus operandi for the "Drone" weapons that the Ancients seem to favor. A cephalopod-esque guided missile weapon about a meter long, capped in some sort of energy-channeling ram head that can bore a hole clean through anything it hits. Against smaller targets, only one or a few are used. Against capital ships, swarms are deployed. The weapons are sometimes recoverable after use since they don't work by exploding.
- The Rashomon: "Sunday"
- Real Dreams Are Weirder: "Doppelganger" has a bunch of alien-induced nightmares, so naturally McKay feels the need to tell everyone about his perfectly ordinary Moby-Dick-inspired nightmare.
- Reality Has No Subtitles: Radek would occasionally rant in Czech about something with no subtitles provided.
- Reality Warper: John Sheppard in "Home" was the first person to discover their reality was faked by the fog aliens. It is heavily implied that Sheppard's instincts are what alerted him to this before McKay, who would only discover the truth due to facts.
- It's also implied that it's Sheppard' strong Lantean heritage that allows him some pretty strong mental barriers.
- Really 700 Years Old: "Todd" is at least ten thousand years old, such that he actually remembers the war between the Wraith and the Ancients!
- Real Men Get Shot: When McKay asks if the rope burns on his hands are going to leave scars in "Trio," Keller remarks that chicks dig scars.McKay: Not the chicks I dig.
- Realpolitik: When the heroes are put on trial for their previous actions, Sheppard basically argues that they are not fighting for right or wrong, but rather they are fighting for themselves.
- Reasonable Authority Figure: Col. Caldwell. At times he is even more reasonable than Weir.
- Red Oni, Blue Oni
- Elizabeth and Sheppard during the first three seasons.
- Ronon and Teal'c in the episode "Midway".
- Red Shirt
- The season one finale features three characters isolated on an Ancient weapon satellite. The writers knew they were going to kill somebody, so they had all three characters wear red.
- In "Midway", three scientists are in the station control room when they are boarded by the Wraith: Bill Lee, who had been introduced years ago on SG-1, Dr. Kavanagh, recurring since season one of Atlantis, and Scott Dempster, who was introduced in this episode with only a single line. Scott Dempster dies.
- Red Shirt Army: The crew of Ancients who briefly resumes control of Atlantis before the replicators hand them their collective ass.
- Regularly Scheduled Evil: The vampiric Wraith harvest human worlds in the Pegasus Galaxy at regular intervals and hibernate in between the cullings of their prey to allow the human population to recover. The Pegasus humans figured out the Wraith's schedule at some point, and the more advanced societies made preparations to prepare for their arrival. When the Atlantis expedition inadvertently awakens the majority of the Wraith, the schedule is bumped up considerably—to the point that the abundant Wraith suffer food shortages and later start to feed on each other.
- Religion of Evil: The Wraith worshippers believe that their vampiric overlords are godlike beings. The religion itself venerates culling of humans, mindless obedience to the Wraith and a prophecy foretelling the end of all human life. The Wraith themselves just consider it a useful tool to instill complete loyalty in their followers.
- Reentry Scare: On more than one occasion.
- Remember When You Blew Up a Sun?: Doctor McKay's lovely talents for destruction of innocent random systems is continually referenced to remind him of his failures and hubris.
- Replacement Flat Character
- Kavanagh is a Replacement Flat Character to McKay, where the shallow role being filled is "recurring jerkass scientist who disagrees with the friendlier main-character scientist, and is always wrong".
- Colonel Ellis is a Replacement Flat Character to Colonel Caldwell, where the shallow role being filled is "ship captain and Obstructive Bureaucrat from the SGC".
- Mr. Coolidge, a new member of the I.O.A., is described as "much less pleasant" than Richard Woolsey, the resident Obstructive Bureaucrat of SG-1 and Atlantis.
- Retroactive Wish: In the pilot.
- Revival Loophole: Used to save Sheppard in "Thirty-Eight Minutes".
- Ridiculously Human Robots: Played for laughs in "Be All My Sins Remembered". Rodney McKay devises a plan to destroy the Asuran homeworld by introducing a nanite-made weapon, but the "simple" design proves so much more difficult to construct from the ground up than the more complex "humanoid" one (for which the machine already has blueprints) that he creates FRAN, a sentient, living weapon Robot Girl. She enthusiastically helps with the planning and is joyous that she'll be destroyed in the mission, which seriously creeps out McKay.McKay: I should never have given it speech.
- Robot War: Double subverted. When the Ancients determined that their Replicator creations were more trouble than they were worth they bombed them out of existence. Thanks to more robust programming than most other examples of this trope, the Replicators could only sit there and take it as their programming would not allow them to even attempt to harm their creators. They rebuilt, though, and this problem was inadvertently fixed by one of the protagonists.
- Royal Brat: Harmony in the episode of the same name.
- Royally Screwed Up: The family of the Lord Protector in "The Tower", where the son is poisoning the father to claim the throne sooner, and would have to immediately kill his sister after he assumed the throne to prevent the chance of her giving birth to an heir with a stronger ATA gene than himself.
- Running Gags
- Aiden Ford sucks at naming things.
- Asking Ronon if his gun is set to stun.
- Dr. Zelenka griping in Czech when he gets frustrated.
- Rodney referring to Sheppard as "Kirk" when he thinks he is hitting on women.
- Someone pointing out that McKay is Canadian when he pronounces a ZPM as Zed-Pee-Em.
- Sacrificial Lion: Dr. Peter Grodin, in the season one finale.
- Sadistic Choice: Elizabeth is faced with a few, usually concerning John. Specifically, at the end of Season 1 when she had to decide between John going on a suicide mission to blow up Wraith hives, or keeping him alive and Atlantis being destroyed.
- The Scapegoat: Sheppard's team becomes this in "Inquisition" for the new Coalition of Planets. Not that a lot of their complaints are not justified, mind you, but all the Coalition really wants is someone to blame for all the shit they have gone through with the Wraith in recent years. They cannot do anything about the Wraith, and the Ancients are not around, and they are perfectly aware the expedition as a whole is too powerful to challenge. Thus, they decide to throw a trial for just Sheppard and his team, so they at least feel like they are doing something.
- Scarpia Ultimatum: Michael offers to not destroy Atlantis if Teyla willingly accompanies him and brings her son with her. She is willing to do so, but knows that Michael is not trustworthy and demands that he deactivate the self-destruct first.
- Schmuck Bait: Clone-Beckett pulls this on a Wraith Commander, goading him into feeding on him... then reveals to the collapsing Wraith that Beckett has the Hoffan virus.
- Schrödinger's Butterfly
- The first season episode "Home". It concludes with the mist assuring them that they are back in the real world.
- "The Real World". It is probably back to reality by the end, but Sheppard remarks that for all he knows, it has just switched to his fantasy.
- Screams Like a Little Girl: Rodney in second season's "Sateda", when he gets hit with an arrow.
- Screw the Electric Bill!: It routinely displays the entire city lit up despite only having a few hundred people on it, and despite the fact that looking for new ZPM's to power the city is a regular plot driver. It may simply be a scale thing, though. Each ZPM has enough power to open a wormhole to another galaxy, and they have Naquadah reactors with them (which are basically enhanced miniature nuclear reactors). It may just be that turning off the lights to conserve energy for whichever critical system keep draining these would be like turning off a faucet to save the water you need to keep Niagara falls thundering...
- Seinfeldian Conversation: When they are trapped in a Puddle Jumper and awaiting rescue, doctors Lee and Kavanagh spiritedly discuss the merits of Michael Bay's Pearl Harbor. Lee is disdainful of the project, but Kavanagh believes that the film has "weight" and will become appreciated in time.
- Semper Fi
- Colonel Marshall Sumner, the original commander of the military forces of the Atlantis expedition, was a member of the United States Marine Corps.
- Sergeant Bates, who Dr. Weir appointed as head of Atlantis security, frequently clashes with the more laid-back Air Force officer John Sheppard throughout the first season.
- When the SGC gets a ZPM and sends a relief military force to protect Atlantis from the Wraith, they are commanded by Colonel Dillon Everett, USMC.
- Send in the Clones: Beckett from "The Kindred" on forward.
- Sexiled: When Carson and Allison Porter are flirting (very obviously) in "Whispers", Sergeant Dusty leaves to secure the perimeter and explains that she will be back in twenty minutes, unless she sees a sock on the door.
- Shadow Archetype: John Sheppard. His Afghanistan-visions in "Phantoms", Crystal-Entity Sheppard "Doppleganger" and Hallucination-Kolya in "Remnants" all hint that there is a part of him that really wants to punish himself.
- Shoot Everything That Moves: O'Neill gets annoyed with Woolsey continually calling out "General, is that you?" when he hears something. So when he needs to go activate a control in a flooded area, he hands Woolsey a gun and says, "If something is coming, then it isn't me. Don't call out to it. Shoot it."
- Shoot the Dog: Michael.
- Shoot the Hostage Taker: Kolya has Weir as a hostage and is trying to drag her through the Stargate, betting Sheppard won't risk it. Sheppard calmly puts one in his shoulder and sends him through the gate without Weir.Sheppard: I will shoot you if you don't let her go.Kolya: And risk hurting Doctor Weir?Sheppard: I'm not aiming at her.
- Shot in the Ass: In "Sateda", McKay gets shot in the rear end with an arrow.McKay: THAT DID NOT JUST HAPPEN!
(later, in infirmary)
Beckett: You have an arrow, Rodney, in your gluteus maximus.
McKay: (on Morphine) Gluteus maximus... Gluuuteus maaaximus... Oh my god! That's my ass isn't it?
(Wraith HUD disappears)
- When asked by the Athosians where they came from, Sheppard tells them; "From a galaxy far,far away".
- In the second episode of the first season, Sheppard looks at the size of the incoming monster of the episode, looks at the proposed containment unit for it and says "We're gonna need a bigger boat."
- In "The Defiant One" Rodney calls Sheppard "Kirk" when he wants to do battle with the Wraith that they discover. This also leads into a Running Gag of referring to Sheppard as Kirk when he gets involved with alien women.
- A frustrated Rodney once refers to Ronon and Teyla as Conan and Xena
- In Episode 10 of the Second season, while piloting a Wraith Dart, John Sheppard gives us this immortal line.
Sheppard: We were getting along so well.
("Autopilot Engaged" appears on the computer screen)
Sheppard: Oh, Autopilot? Nononono, No!
("Dock Procedure Loaded and Activated" appears on the computer screen)
John Sheppard: R2, I need you to turn the Autopilot off.
Neera: And the clowns?
- In "Outcast", Dr. Lee is trying to think up how to destroy the Replicator that is on the loose, and mentions that if it was a movie they would drop it into a vat of molten lead or a volcano. This, of course, gave Sheppard an idea.
- Part of Rodney's long numerical computer password, as revealed in season four's "Quarantine," is 42, which Sheppard explains to Teyla is the answer to the Great Question of Life, the Universe and Everything.
- In "Quarantine", Sheppard is preparing to free climb four floors up the outside of the main Atlantis tower. When Teyla asks if this is possible, Sheppard replies that "Batman did it all the time!" As he is completing the climb — and has just saved himself from falling to his death — the Batman theme music subtly plays as he pulls himself onto a ledge.
- In "The Hive", Sheppard is talking to a fellow prisoner, Neera who turns out to be a Wraith-worshipper placed there to pump Sheppard for information, and mentions his fear of clowns.
Sheppard: Clowns? Oh yeah, the clowns. Well, we fight them, too. Entire armies, spilling out of Volkswagens. We do our best to fight them off, but they keep sending them in.
- Dr. Bill Lee comparing relaying a message from the SGC to a small planet on the edge of the Milky Way, to the Daedalus then to Atlantis, to that of the "Twilight Bark" from 101 Dalmatians, his kids' favourite movie. When no-one gets the reference, he instead refers to the the beacons being lit in The Lord of the Rings. Which everyone then understands.
- Large parts of season three's "Vengeance" is a reference to the first two Alien movies.
- In the season two episode "Coup D'Etat", a Genii soldier contacts Atlantis, informing them that he and his men have seen several teams on various worlds dialing the symbols for the Atlantis gate. From this, he adds, he can conclude that "the rumors of their city's demise have been greatly exaggerated."
- Shut Up, Hannibal!: A subdued example. When a group of living Ancients is rescued and demands the return of the city, one of the things their leaders bring up is how the expedition awakened the Wraith. Woolsey is quick to retort that it was the Ancients' own negligence that made the Wraith such a threat in the first place. Though she still sticks to her demands, that marked the end of any attempted moral high ground on her part.
- Sibling Team: Dr. McKay and his sister, Jeannie Miller - a.k.a. David Hewlett and his sister, Kate Hewlett.
- Single-Stroke Battle: Ronon and a constable of the Lord Protector in "The Tower".
- Skip the Anesthetic: When the team first met Ronon, he revealed he had a tracking chip at the base of his brain stem that the Wraith used to track him down for sport. As he didn't trust the others, he insisted Dr. Beckett perform fairly intense surgery with him awake, sitting up and holding his gun. Subverts the norm as he passed out from the pain once the chip was removed.
- Sleeper Starship: The team once found an Ancient Battleship with the crew in stasis and using a virtual environment to interact. Unfortunately they had continued to age slowly and were too old to leave so they ended up performing a mass Heroic Sacrifice.
- The Smart Guy: Dr. M. Rodney McKay, obviously.
- The Sociopath: The Crystal Entity from "Doppleganger" is explicity referred to as such because of how much it enjoys scaring people, quite literally, to death in their dreams.
- Some Call Me "Tim": Sheppard loves this trope. Therefore we have the Wraiths Steve, Bob, Michael and Todd.
- Sorting Algorithm of Evil: The team woke up the Wraith and later turned on the even more dangerous Asurans' hostility switch. Nice Job Breaking It, Hero! indeed. The last episode of Atlantis was essentially the concept of when the villains skip a few levels past where the heroes are expecting.
- Spinoff Sendoff: The pilot starts with a visit to the arctic expedition by SG-1's Jack O'Neill and Daniel Jackson.
- Space is 2-D (2-D Space): Generally played to the trope, but jarringly averted on a couple of occasions where a jumper exits a gate at totally "wrong" angles to everything else in the scene - often remaining as such until they must dock with a ship, where it then rotates into synchronous planes.
- Spock Speak: Teyla rarely uses contractions in her speech, if ever. Compared even to other Pegasus natives the Athosians appear to be a very formal in their speech.
- Spotlight-Stealing Squad: Rodney McKay. He receives the most backstory and character development over the course of the series, including some backstory for his own sister, who appeared in several episodes. It made everyone else look static and flat in comparison.
- Superman Stays Out of Gotham: The whole setting of the Pegasus Galaxy was created specifically to avoid having the Expedition getting bailed out by SG-1 in a crisis.
- Super Serum: Lieutenant Ford (and briefly Teyla and Ronon) gains increased strength and a resistance to Wraith stunner technology after he is injected with an enzyme that the Wraith produce as part of the feeding process. Too bad it also drove him insane.
- Take Off Your Clothes: McKay, Carter and Dr. Keller are trapped in an abandoned mine, and McKay suggests that everyone disrobe so they can make a rope by tying their clothes together. Keller immediately gets started while Carter responds by producing a coil of actual rope which was in one of the boxes. McKay is clearly disappointed.
- Techno Babble: An in-universe example while stalling for time:Weir: Find another problem with it. Tell them that the power loop interface isn't jiving with your walkabout, something.
- Teenage Wasteland: One episode featured a tribe of kids from age 25 and down. After they reached 25 they committed suicide, but only because they had to keep the population small due to being kept safe by a shield that was slowly becoming smaller. But they didn't know that...
- Teleport Interdiction: The crew of the Daedalus, in their first appearance, plans on destroying a bunch of Wraith ships by using Asgard beaming technology to beam nukes onto them. It works the first three times they try it. After that, the Wraith figure out how to jam the beam.
- Team Dad / Team Mum: Sheppard and Weir. The two of them make it VERY clear that Atlantis is their city and they will protect its inhabitants at all costs.
- Telepathy: The higher castes of the vampiric Wraith have telepathic abilities, used mostly to control the far less intelligent Wraith soldiers, though Queens are strong enough to control humans as well. They were also able to project illusions in the pilot, but this trait was quickly removed.
- 10,000 Years: the Earth-Atlantis Expedition returns to Atlantis and the Pegasus Galaxy 10,000 years after the Lanteans lost the Wraith war, sank Atlantis, and retreated back through the Stargate to Earth.
- Then Let Me Be Evil: Michael. Immediately after the experiment designed to stop him being Always Chaotic Evil, how do they treat him? Like he is Always Chaotic Evil. After several attempts where he tries to say "What the hell, heroes?" and do something appropriate before they screw him over again, he just goes nuts and becomes an Evilutionary Biologist, blaming the heroes, rather sensibly, for everything he has become.
- There Is No Kill Like Overkill: When removing a parasite from McKay's brain, Keller advises Ronan to ready his weapon. As soon as it is removed, he blasts it. The other characters call him on the overkill, to which he points out that Keller told him to.
- Third Wheel: Although not explicitly shown, Sheppard becomes the seventh wheel by the season finale with all his friends — Woosley was never really part of the True Companions — getting together with someone. (Rodney with Jennifer, Teyla with Kanaan and Ronon with Amelia).
- This Is Something He's Got to Do Himself: Subverted in "Sateda". Ronon tells the rest of the gang that if they kill the Wraith "General", he will kill them. Ronon specifically says he wants to do this himself, as the Wraith leader had destroyed his civilization and then hunted him like an animal for seven years. He gets his ass handed to him and only survives because Beckett blows away said Wraith with a drone weapon. Ronon is actually relieved. This was a notable piece of character development, as everyone else expected him to be very angry.
- To Serve Man: Human beings are the Wraith's sole food source (specifically their Life Energy), and the human societies in Pegasus are treated like cattle.
- Tomato in the Mirror
- The title character in "Michael" realising that he is not a human with amnesia, but he is actually a Wraith.
- Halfway through "This Mortal Coil", the primary cast discovers that they are all Replicator-built copies of the Atlantis staff.
- Touched by Vorlons: Elizabeth Weir becomes a Replicator.
- Too Clever by Half: McKay
- Took a Level in Jerkass: The Vanir Asgard who are incredibly ruthless compared to their Ida Galaxy cousins.
- Trailers Always Spoil: The Italian trailer for season 5 outright revealed that Atlantis would return on Earth.
- David Hewlett's role as Dr. Rodney McKay originated in SG-1, where he was brought in as a pseudo-rival to Samantha Carter in two separate episodes. The character was originally not supposed to feature in Atlantis, but when Hewlett joined the cast the writers decided to resurrect the old character instead of having him play a new character.
- Craig Veroni, who played Dr. Peter Grodin, first appeared in the Stargate-verse as an unnamed character in "Grace", a seventh season episode of SG-1. It was never confirmed if this was an early appearance by Dr. Peter Grodin, or the actor being cast in two distinct roles.
- Dr. Lindsay Novak, a scientist aboard the Daedalus with a habit of hiccuping while stressed, first appeared in SG-1's eighth season episode "Prometheus Unbound" before becoming a recurring character in season two of Atlantis.
- Samantha Carter was one of the lead characters on SG-1 for all ten seasons, joining the main cast of Atlantis in season four after SG-1 was cancelled.
- Woolsey taking over from Carter as head of the Expedition in season five after previously having appeared in SG-1. His entire character redemption arc is also carried over, with him learning to lighten up, stop being such an Obstructive Bureaucrat and why bending the rules on occasion can be beneficial to the success of the mission.
- Uncertain Doom: Lt. Ford was last seen on an exploding ship, but it's never confirmed that he is dead.
- The Unfettered: Acastus Kolya
- Unresolved Sexual Tension: Elizabeth and Sheppard.
- Unspoken Plan Guarantee: "Return Part II"
- Unwinnable Training Simulation: The episode "Progeny" has the Replicators trick the team into believing that they have gone back to Atlantis, where the city is attacked by nine hive ships. Sheppard stays behind to trigger the self-destruct as fifteen more hive ships join the fight.
- The Usurper: "Harmony" revolves around a plot by the sister of the prospective-queen trying to have her sister killed so that she can claim the throne.
- Vampiric Draining: The Wraith take your Life Energy through their hands. It is stated to be the only way they can gain sustenance and a recently fed Wraith also gets an extra Healing Factor. This Life Energy is stated to have some kind of biological basis, but it basically behaves like magic with people growing old during a feeding and the process being reversible.
- Video Game Caring Potential: When Keller, Rodney and Ronon bring a wounded young girl back to Atlantis, Rodney tries to teach her to play Duck Hunt, but she refuses to shoot the adorable little ducks.
- Video Game Cruelty Potential: An in-universe example in which Sheppard and McKay find an ancient game in Atlantis in which they are able to control two neighboring countries. Two years after they first played the game, they find out that the countries are real and that they have been changing the lives of real people. Then Lorne and Zelenka get in on it, despite knowing better. Weir has to be the voice of reason.
- Villain Decay: The Wraith seem to go through this, especially in the last couple of seasons, due to both Lowered Monster Difficulty and the story changing the emphasis from "the Wraith slowly wiping out all Pegasus humans" to battles against Eviler Than Thou enemies such as the Replicators and Michael. Todd also helped with the Villain Decay, because he gave a lot of insight into Wraith culture, and it was decided not to make them as evil as we were first led to believe.
- This might also have something to do with the fact that for the first two seasons, the Expedition actually knew very little about the Wraith and the main perspective on them came from the residents of Pegasus who had a superstitious dread of them as an omnipotent force of evil, and the Ancients in their last stand, when the Wraith were overwhelming them.
- Villain Episode: The series shows the POV of a Wraith named Michael in the eponymous episode, which makes the main characters look morally ambiguous, if not downright evil, for their treatment of the Wraith-turned-human. The sympathies of the audience remain with Michael during most of the episode, and for a large part of the fanbase, well after Michael became a threat to the team in his own right. Then he lost all that sympathy when he became the most evil antagonist in the series, and a Hypocrite to boot.
- Villainous Crush: Michael becomes obsessed with Teyla, and has created this fantasy where, after he abducts her, she will voluntarily choose to remain with him. Guess who kills him.
- Vitriolic Best Buds: Sheppard and McKay live this trope. Zelenka and McKay have a similar dynamic. Really, anyone and McKay could qualify.
- Viva Las Vegas!: The penultimate episode "Vegas" is set in the city, where John Sheppard is instead a police detective investigating a series of grisly murders committed by a lone Wraith. It later turns out to be an Alternate Reality Episode in which Sheppard's life turned out somewhat differently from the one we're familiar with.
- Warring Natures: Michael. It doesn't work out very well for him.
- We Have Reserves
- Both the Wraith and the humans of the Atlantis expedition point out that no matter how many Wraith ships they destroy, the Wraith will just send more. Back during the war with the Ancients, this was a viable Wraith strategy, largely because they had cloning factories.
- When the Genii have Sheppard and McKay cornered in "Harmony", the Genii commander points out that they cannot escape since they have limited ammunition but he has unlimited men. Tellingly, once he is dead the Genii forces beat a quick retreat.
- West Coast Team: To the original Stargate SG-1, which it ultimately outlasted.
- Wham Shot: After the successful destruction of the Asuran homeworld in "Be All My Sins Remembered" by the Tau'ri-Wraith-Traveller alliance, the last shot of the episode reveals the apparently still alive Elizabeth Weir clad in villain gear and commanding a Replicator ship and pronouncing a rather ominous Wham Line.
- What Does This Button Do?: McKay claims exclusive rights to this trope, reasoning that he is the only person competent enough to fix what will almost inevitably go wrong upon doing so, while others will turn to him for the same. In "Sunday", this turns out to be painfully true.
- What Happened to the Mouse?: In the mid-season two-parter for Season Five, Col. Caldwell is, as usual, in command of the Daedalus. After being knocked unconscious along with the rest of the bridge crew during a mutiny, he vanishes completely and is never even mentioned during the second half, while Mr. Woolsey casually takes over and starts issuing orders without being once questioned as to his authority to do so or his competence to command a space-going battlecruiser.
- What the Hell, Hero?
- A clip show in which the Pegasus Galaxy call the Atlantis Expedition out for all the chaos they have caused with a panel of three judges. Subverted since the reasonable one ultimately agrees with them when the Expedition makes their case, the emotional one isn't listening and was never going to, and the swing vote is corrupt and happily changes sides in exchange for a suitably large bribe.
- "Michael" loves to point this out, that for all their preaching about morality, in regards to torturing and experimenting on prisoners, the Expedition violated it several times because of the flimsy justification that human rights do not apply when the enemy isn't human. This loses a bit of its punch when you consider that he promptly did the exact same thing, on a far grander scale, slaughtering entire planets to create his Hybrid army, while the Expedition was largely isolated and up against an entire galaxy full of Wraith, meaning that it fell into I Did What I Had to Do territory.
- What You Are in the Dark: In "Harmony", with the Genii between them and their goal, Sheppard and McKay decide that it is too dangerous to continue with the rite of passage to make Harmony the queen. When they ask why it even matters, since nobody will know that she did not technically finish the rite, she points out that she will know.
- Why Are We Whispering:Dr. McKay: [whispering] They're scanning for us.Dr. Weir: [whispering] Why are you whispering?Dr. McKay: [whispering] I don't know, it just seemed like the right thing to do.
- Wicked Cultured: In "Condemned", the team goes to a planet whose leaders struck a deal with the Wraith. The Wraith who regularly visits the planet enjoys fine cuisine and wines, despite the fact that they provide no nourishment for him. He considers himself a more enlightened and civilized Wraith than his brethren for allowing the planet to live in peace (instead of being constantly submitted to genocidal harvests) in exchange for a small but steady food supply. He admits he does enjoy his dinners with the magistrate, to whom he is courteous and polite, but since he's still a life-sucking monster this is capped off with things like the Wraith pointing out that the previous cook was tastier than his meals, and he threatens to annihilate the whole planet unless they give him more people to feed on so he can "provide" for his Wraith friends.
- Wild Card: Todd the Wraith (real name 'Guide', apparently), oh so much. The only thing he can be sure of doing is what's best for him - and even then, that's not entirely certain.
- With Great Power Comes Great Insanity: The Wraith enzyme, which confers increased strength and a resistance to Wraith stunner technology, also mentally imbalances the human mind. Rodney McKay explained that, while under the influence of the enzyme, it seemed to him like everybody else was crazy.
- Withholding Their Name: When telepathic Wraith get captured for interrogation or just become recurring characters, Colonel Sheppard randomly assigns human names to them so they can be called something other than "that Wraith". The Expanded Universe novels reveal that Wraith have names that they use among each other (Todd's, for instance, is Guide), but they're apparently based on their roles in society and/or how their minds "feel" to each other telepathically, which means they have no way of communicating their names to humans even if they wanted to.
- Within Parameters: Leading to a solar system blowing up. (5/6 of a solar system!)
- Worst Aid: When Ronon was impaled through the shoulder by a piece of shattered glass during a Replicator attack on the city, he told the medical attendant working on him to just pull it out. Knowing that that would only make things worse, the attendant refuses to do so, and stops Ronon when he is about to do it himself.
- Worthy Opponent: When Ronon dodges the second Booby Trap in "Tracker", all he has to say of the Runner he is tracking is "he's good."
- Wouldn't Hit a Girl: Sheppard won't fight back in "Travellers" despite being kidnapped and repeatedly assaulted, despite the fact that as a soldier it is his duty to escape. The reason? His captor is a woman.
- Wrong Genre Savvy: In "Quarantine", when Sheppard is locked in a room with the pregnant Teyla he becomes concerned since, in the movies, the pregnant woman always goes into labour in that scenario. However, since this is a sci-fi adventure instead of a romantic comedy or personal drama, her baby waits for a later episode.Sheppard: It's just that, every time one of these things happens in the movies, the pregnant woman goes into labor.
Teyla: I am still a long way from my due date.
Sheppard: Yeah, it's the same thing in the movies and then, wham.
- You Are Not Alone: How Sheppard motivates Elizabeth to overcome the nanite infection in "The Real World".
- You Can't Go Home Again: Only held for a season, thanks to Stargate Command getting those spiffy intergalactic hyperdrives from the Asgard and a new ZPM. They later have the McKay-Carter Intergalactic Gate Bridge for a while, but then it is destroyed and they go back to combined gate/interstellar travel.
- You, Get Me Coffee: In "Whispers", Sergeant Dusty mentions that she transferred to Atlantis from the SGC because there are "more bad guys that need killing," but Sheppard keeps assigning her to guard Carson and Porter instead of investigating the mystery of the deadly monster experiment.
- You Have Failed Me: In "Irresponsible", when one his subordinates reports that Sheppard managed to escape, Kolya draws his pistol, points it at the reporting officer and pulls the trigger... which does nothing. The subordinate thanks Kolya for his life and goes back to duty, vowing to do better. Kolya then turns to another subordinate and orders him to have his gun fixed.
- Your Worst Nightmare: In "Doppelganger", an entity jumps from an alien crystal to Sheppard, then from him through various cast members, causing vivid nightmares starring a sociopathic Sheppard. The entity only scares people at first, until killing the psychiatrist Dr. Heightmeyer in a falling dream where she hit the bottom. The episode gives insight into each of the team members greatest fears. McKay's fear is being eaten by a whale, Teyla's is nobody trusting her and wraith darts taking her father, Ronon's is everyone around him disappearing and being buried alive, Keller's is the chestburster from Alien, and Sheppard's is his own failure to protect the people he cares about. And clowns.
- Zeerust: Averted most of the time, but the Ancient Ships are, design wise, terribly dated and unimaginative for a race that was supposed to have the most advanced technology known to exist. The ships really do speak late '90s early-2000s, before the technological and engineering advances of five to ten years ago. Considering that we know that all the Ancients needed to do was to slap hyperdrive and sublight engines to a structure covered in a shield (like Atlantis itself), the Ancient ships don't look that much more advanced than the Daedalus-class ships from earth - though their firepower is, for the most part, considerably greater until the Asgard upgrade them.
- Zerg Rush: How the Wraith defeated the Lanteans and generally the way they like to roll. Since they had the numbers advantage even before they involved cloning factories, you can see why this would be considered a viable strategy.