John Sheppard: Heroic, selfless badass ready to risk everything to save Atlantis and those he cares about? Or ruthless sociopath willing to commit any number of murders under the justification of "protecting his people"? He could be quite coldly manipulative at times. A noteworthy example was in "Miller's Crossing" when someone had to sacrifice themselves to a Wraith in order to save McKay's sister. McKay volunteered but Shepherd refused to let him. Instead, without even blinking, he recruited the grieving father who'd injected her with the nanites (having done so in order to motivate McKay to save his daughter's life), and talked him into sacrificing himself.
There is a trend for the characters to fit both their standard interpretation and their Alternate interpretation concurrently, usually changing it up between episodes. This tends to be because the episodes are inconsistently written such that some are very intelligent and sensitive to the issues surrounding sentient life equivalency and the progression of humanity, and some are... not.
Ass Pull: The wormhole drive in the finale. One of the producers commented that its use in the finale was meant to set up the viewers for its use in an upcoming Atlantis movie, meaning that the writing crew tried to pull a Chekhov's Gun out of their ass.
Base-Breaking Character: Rodney McKay. You either like that the smart guy is the one who saves the day or find him incredibly grating. The fact that it is often very easy for one person to be in both camps at the same time makes things... confusing? There is also a persistent fan theory that as the show went on, Rodney evolved into the Author Avatar for the writers, especially with the amount of backstory and screen time he received in comparison to the rest of the cast. (If you subscribe to this theory, it makes a hell of a lot more sense about Dr. Keller being paired with Rodney... of course the Creator's Favorite and Author Avatar would get together.)
Cargo Ship: In some circles John/Atlantis or Elizabeth/Atlantis (or both). They're both Married to the Job, John has an incredibly powerful ancient gene and connection to the city and Elizabeth in more than one reality sacrificed herself to preserve the city and in Season 3 went into Heroic BSoD when they were forced to leave.
Complete Monster: Even amongst the monstrous Wraith species,note As compared at least to Todd, who displays some awareness that he's an apex predator that hunts sentient beings. these two stand out:
Michael Kenmore is a former Wraith who guiltlessly kidnaps one of the humans who had helped him, in order to painfully feed on her energy when he rediscovers his origins. Although his attempts to give Atlantis to his species fail when they try to kill Michael for his time as a human, he returns as an experimenter trying to create a "perfect" race that is mindlessly obedient to him. Creating a race of Animalistic Abominations, Michael engineers them by having human test subjects fatally drained of their life energy. Releasing a virus on multiple inhabited worlds, Michael kills countless humans and spitefully leaves the survivors infected to poison any Wraith who attempt to feed on them. Michael also creates a clone of a deceased person, which he tortures and experiments on for months; and kidnaps an entire tribe of people to turn them into his new violent experimental race, the "Hybrids". Kidnapping a pregnant woman, Michael plans to harvest the baby's unique DNA for his Hybrid project and kill the mother after birth. When Michael manages to gain control over Atlantis, he again attempts to kidnap the woman and her now-born baby, and spitefully blow up everyone else on board.
The Wraith "King" or "General", from season 3's "Sateda", is a sadistic Blood Knight who commands a Hiveship, having committed the taboo of murdering his Queen to usurp control of it from her. Harvesting countless planets over the centuries, the King has destroyed Ronon's home world, annihilating the entire population, including Ronan's lover. Implanting a tracking device in Ronon to hunt him from planet to planet for sport, the King destroys any world where he takes shelter. Returning to Ronon's home world to kill him on it, the King mocks him for the death of his people.
Designated Hero: Although our heroes are in general good guys who try to do the right thing, there are quite a few times where what they do is at the least soaked in Moral Dissonance and at the most downright evil - sometimes contradicting previous characterization to do so. When written at their worst they have a very human-centric perspective about sentient life such that only human and human-like beings matter, and are disturbingly willing to exploit, manipulate, experiment on, mass murder (as in killing huge numbers in cold blood) and double-cross anyone or anything that poses a threat or can be labelled an enemy species (even taking into account the requirement to act cautiously and even proactively against threats when they present themselves), even treating one of their own expedition similarly when they come back as a Replicator.
In "Infection" where Sheppard comes across Todd's completely defenceless diseased Wraith hive ship where his entire crew - now having undergone a gene therapy where they can no longer feed - are in stasis pods. Originally the plan was to just leave them or blow up the ship, However, because of the ship's malfunctions there is an off-chance that they might break free from the pods. Sheppard's solution? Suffocate the hundreds of Wraith in their pods and use C4 to blow up any pods that are unresponsive to the "suffocate their occupants" command. The Team decided that if the gene therapy really was effective at killing Wraith, they should try to disseminate it to as many Wraith as possible for use as a biological weapon.
On the other hand, when the non-human beings in the galaxy are mostly composed of psychic vampires who eat humans (only humans) and enjoy it, and the Pegasus version of the Replicators, who have repeatedly almost devoured and destroyed two entire galaxies - and in the case of the Pegasus versions, have at the very least shown an inclination towards Mind Rape (on good days) and omnicide (on bad ones) when dealing with humans, you can kind of see why they might be willing to cross some lines.
Designated Villain: Bates, Kavanaugh and Ellis tend to end up in this role. They usually have legitimate concerns or complaints, but because these are expressed, usually against the main characters, in a way that is distinctly in favour of their own self-interest and usually to the detriment of others that they are willing to sacrifice, the characters are presented as reactionary jerkasses. Bates seeing Teyla as a security risk and willing to essentially exile her people, hence putting them in great danger in order to protect the expedition members; Kavanaugh complaining to Weir about Weir being somewhat rude to him in front of his team when he prioritises and focuses on a course of action that puts the safety of Atlantis first no matter the risk assessment or loss of life (although what is more the issue is that in an emergency when time is crucial and lives are depending on him and his team, he takes time out to go and complain to Weir about her behaviour and how it bruised his ego, dismissing and mocking her authority in the process); Ellis undercutting Weir's authority behind her back because she challenges his opinion and his own authority, and wanting McKay to cut the exposition and get to the point in a way that pointedly bullies and demeans him). There is also a trend of portraying Kavanaugh, in his few appearances, as a coward even though every time he is up against a situation in which his fear is perfectly understandable, although he does consistently advocate a course of action that will save himself and whoever is with him while sacrificing other people, sometimes even when the risk to himself is minimal.
Ellis isn't so much a Designated Villain as a Jerkass who likes to bully and harass those who make him feel inferior. He's a good man, a competent officer (as befitting his rank), and takes pride in making the right call, but doesn't like it when people who are smarter than him have an idea or explanation that he finds difficult to grasp. Both times he doesn't tell McKay to cut the exposition and get to the point, he insults and harasses him for giving a long explanation, often one that is necessary to understand what he's trying to tell him. The first time, he cut him off and then McKay had to go back and explain the entire thing all over again because he didn't understand. The second time he outright bullies and degrades Rodney in a meeting so severely that Samantha Carter has to tell him that if he ever talks like that to someone again she'll have him forced off Atlantis. And that's really saying something; Sam wouldn't defend Rodney like that unless what Ellis was saying was absolutely unacceptable, particularly considering that he and she are of equal rank.
As for Kavanaugh, while he does come up with semi-decent ideas, he is also: spectacularly irritating; of the belief that he's much smarter and more important than he is - while he's smart, he's not McKay/Carter smart, as he seems to believe, nor is he an especially important member of the science team, let alone the expedition at large; prone to putting his ego before everything else, even in a crisis. His complaint to Weir in his first appearance isn't about his idea not being taken seriously, it's about his ego being bruised. He also claims, when the discussion is very much over, that it isn't, assuming that he can dictate to Weir, completely disregarding her authority.
Michael is a subject of some contention with this trope. Many people express their disapproval of how Michael is treated, and/or focus more on the terrible way he was turned into a villain rather than the aftermath. As such, it is easy to presume that all this "Kill almost everybody and turn the rest into an unstoppable army of destruction" thing kinda slips their minds and Michael gets the Draco in Leather Pants treatment by default. That said, disapproval of his treatment doesn't mean approval of his actions - and just because the enemy is evil, it doesn't mean the heroes get a free pass to go play at the Moral Event Horizon. In a very straight use of this trope, though, some people do in fact sympathize entirely with Michael and do in fact forget that he ended up as an Omnicidal Maniac who would use a baby to perfect his mindless army, no matter what made him that way.
You wouldn't believe how many fangirls Todd has. Although Todd, despite being a Manipulative Bastard, has saved Atlantis' hide a number of times and has never tried to destroy them (despite multiple opportunities) or use what he has gained from them against them (except for the Attero device incident, and even then, he genuinely thought they'd stabbed him in the back). Although self-serving and human-eating, you. really can't classify Todd as a villain all that much, let alone one of Michael's Omnicidal Maniac caliber.
Engaging Chevrons: Played straight and subverted in "Rising". A big deal is made out of dialing the 8th chevron to actually get to Atlantis. Later, McKay slips into Walter's old "Chevron One... Encoded" routine the first time the Atlantis gate is dialed and gets a dirty look from Weir. After that it's never done again, since the Atlantis gate can be dialed in a matter of seconds.
Also Major Lorne and the gateroom tech. Fandom assigned first names to both of them (Evan or Nick — usually the former — for Lorne and Chuck Campbell for the tech), and the latter became a case of Ascended Fanon.
Depending on the fans preference for gay or straight couples; John/Rodney and John/Elizabeth. The former has a count of 2,516 entries on fanfiction and the latter 2,364. (In comparision John/Teyla only has 1,184.)
Ronon/Teyla are also far more popular than the canon Teyla/Kanaan.
Ronon/Keller was better received than Keller/Rodney, it didn't interfere with shipping McKay/Sheppard, and Ronon was pretty popular so fans liked the idea of him getting to be with someone.
Fridge Horror: Sheppard's story in 'Remnants' when the characters control their own hallucinations. While Woolsey and Rodney create innocent and even happy visions of love interests and friends, Sheppard hallucinates Koyla taunting, beating and torturing him for hours on end. (Including cutting off his hand). And when he realizes it's not real? Turns out that he believes he deserves to suffer for everything he's done wrong. Worryingly, the series never returns to this so presumably Sheppard ended the series still drowning in self-loathing and emotionally torturing himself. (Made worse as all his friends have paired off and are living their Happily Ever After).
Funny Moments: Doctor Zelenka returning from the planet of the children in "Critical Mass", and Rodney commenting "Mister Mom... fun with the kids?" (He's covered in facepaint and has straws woven into his hair) Zelenka turns to him and says: "Do not even speak to me!"
Genius Bonus: Genii is the plural form the Latin word "Genius" (no pun intended).
Growing the Beard: All the badass characters either show up or are promoted in season 2: Ronon, Caldwell, Lorne, Sheppard, etc.
Sheppard and McKay are everyone's favorites with scenes that seems to back it up (the end of "Irresistible", for example, where McKay takes a herb that makes people enamored of its user, knowing full well that Sheppard is the only person on Atlantis that hasn't been inoculated against the Pheromones).
Beckett and McKay are great friends and even kissed once while McKay was sharing a body with the mind of a female soldier.
The Sheppard-and-Ronon section of "Sunday" gets very date-y, especially when they're hanging out and drinking beers in Sheppard's quarters and Sheppard asks Ronon if he's seeing any girl or guy.
A Foe Yay example is the relationship between John and Todd (the Wraith), especially when they formed the first human/Wraith alliance to escape a prison together. Though they're basically enemies and don't trust each other, they're friendly enough to work together in several episodes.
Ho Yay Shipping: Most notably, John Sheppard and Rodney McKay. There are some people who watch the show specifically because of this.
The whole Series Finale, with idiot plotholes, stupid character decisions and Ass Pulls all around. To give an idea of the problems in just one aspect of the finale: bringing Sheppard to Earth and not putting him in the chair but letting him pilot a 302 instead because...? Putting the chair not half a mile under what amounts to an icy fortress with one entrance (Antarctica), or a similar easily defendable structure, but in an easily targeted warehouse with no air defence because...? The stupidity of defending the entire earth with a handful of 302s because...?
One thing that becomes really frustrating is that a number of simple solutions to any one of a number of situations present themselves, and the characters steadfastly ignore them with not even so much as a Hand Wave to explain why. For example, when Atlantis finds that upon dialling Earth, the wormhole opens in the modified hive ship, which has a gate inside it, why they don't simply overload one (or even two) of a number of Atlantis's now surplus naquada reactors and throw it through the wormhole to blow up the hive ship is because....? They could have thrown through any number of explosives, over-loaded reactors, energy weapons, shot drones from a puddle jumper, or even overloaded the gate, but they send through one team of people instead... What.
The entire retrovirus subplot in Season 2 & 3. First strike for carelessly leaving the unfinished formula out in the open for a scared little girl desperate for a cure to get ahold of. Then their experiment on a captured enemy Wraith backfires spectacularly and blows the expedition's cover. Then when aforementioned Wraith seems to put the incident behind him and offers himself as a potential ally, the team betrays him again. Unsurprisingly, it backfires just as badly as the first time, and they lose their own Hive ship for the effort.
S01E05, Suspicion: After the team is attacked very early on during numerous excursions by an alien civilization whose biological, technological and/or tactical, strategic, and intellectual capabilities are for all practical purposes completely unknown save for the very barest of details previously obtained from rare surviving eyewitnesses, the only viable explanation for the problem is apparently that someone high ranking among their close allies, who are themselves prey for the enemy and literally require them to help ensure their survival, must be a traitor.
5.14 "Prodigal": Michael and his Hybrids are suddenly afflicted with Idiot Balls in their final appearance to make the All Your Base Are Belong to Us plot last long enough, because Michael technically already wins in the opening. This overlaps with a Villain Ball because Michael stretches out their take-over specifically so he can activate the self-destruct. The mistakes they make are still legion:
Not leaving Teyla unconscious until they're clear of Atlantis by stunning her repeatedly or even restraining her while she's awake so she can't, say, take her mission-critical baby and flee from your grasp at the first opportunity. This can initially be explained by Michael wanting to offer her to join him willingly, but when she refuses, he has no excuse for even risking it.
Leaving all the gate room people, two dozen or so stunned humans (including The Big Guy Ronon), in an unmonitored room with an accessible door panel and a single guard posted at the other side of the door. The Hybrids could have just killed them all to save themselves the trouble of bothering to seclude them after they've been knocked unconscious. They were already planning on blowing up Atlantis anyway, so they had no believable reason to keep them alive beyond plot-required stupidity.
Informed Attribute: Sheppard's reputation as Atlantis's version of Kirk He's definitely a flirt but rarely seems interested in anything more. There are only actually four women things go further with and he doesn't even sleep with all of them. note Chaya was an ascended ancient more interested in mind-melding than sex, he only got together with Teer - who also ascended - when he thought he could never get back to Atlantis, his reaction to Mara offering herself to him was a very bewildered "I did not see this coming" (and he hinted to Elizabeth he didn't sleep with her anyway) and he only kissed Larrin as part of a power-play in between her beating him up. That's less than one woman a year. In fact Sheppard seems more committed to Atlantis than anything else, spends more time flirting with Elizabeth than alien women and is the only main character single by the end of the series.
The Asurans. The Lanteans tried to wipe them out, and the Atlantis Expedition later tries exactly the same because they're dangerous. Its even noted at one point that the reason they're envious of Humanity is because they see us as the favourite son who received all father's attention.
Of course, the "jerkass" part comes into play because their plan to destroy the Wraith was to wipe out their food source; in other words, every single human in the Pegasus Galaxy.
But this only happened because instead of rejoicing in creating artificial intelligence so advanced that it developed consciousness and compassion, and taking out the aggressive programming that made them a threat, the Alterans decided that they were Not Even Human and just wiped them out. After being treated like that its no wonder they are so distanced from biological intelligence: the only ones they knew were Abusive Parents.
Though it is also worth noting that while this isn't exactly out of character of the Alterans, we only hear the Asurans' side of the story.
The engineer in "The Ark" who was awakened to find that his family did not survive. He's completely distraught, and you sympathize with him. When he kills himself by burning himself up in the engines of the shuttle that was supposed to transport the last of his people, it's a little self-centered but still understandable... until you find out that he was trying to vent the entire moon station that he, his people, and the team were on into space via explosive decompression, using up all the fuel needed for the shuttle in the process of trying to kill himself and everyone else, and that in order to save these one thousand people he was complicit in the murder of hundreds of thousands who were slaughtered by atomic radiation in an Extinction Level Event that his people enacted so the project would succeed. Keeping in mind that this is the very last of his entire planet, and that the thousand left include two hundred children.
Bonus lack of sympathy because he helped kill all those people specifically to get a slot on the lifeboat for his own family, and they weren't saved, and he felt betrayed that his coconspirators were willing to let people they didn't care about die. Um. Yeah? I'm pretty sure that was kind of the point of the exercise.
Kolya's feeding Sheppard to "Todd" the Wraith is seen as this by everyone, including Kolya himself.
McKay: Kolya! He could have left you to die! He does not deserve this!
Kolya: Let's be clear, Doctor McKay: no one does.
Turning Michael into a human for the second time, after he's not only sacrificed his own kind but helped the Atlanteans out multiple times, counts as this for some. The fact that the humans don't even think they're doing anything substantially wrong is what makes this even more horrifying.
Killing the Asurans comes close to crossing the horizon.
What Atlantis does to the Asurans who only wanted to Ascend - condemning them to an And I Must Scream fate - goes right over the horizon and keeps on going. Weir in particular stands out, as she was the leader of the group of Asurans and the betrayal is revealed to have been her plan, hence why went through the Gate first to convince them it was "safe" on the other side.
The Ancients attempt to wipe out the Asurans is equally horrifying. When we wished that the Ancients would have cleaned up after some of their messes, we didn't mean through carpet-bombing!
The hallucinations in the season 1 episode "Hot Zone", caused by an Ancient nano-virus.
In "Doppleganger", the malevolent crystal entity that assumes Sheppard's form in people's nightmares, is capable of scaring people to death such as Kate Heightmeyer and provides no real reason for it's actions other than It Amused Me. When it's returned to it's homeworld at the end of the episode, we see that there are hundreds more of these crystals stretching for miles around.
Seasonal Rot: Season 4 and 5. Killing Beckett and Weir got some backlash as Beckett was a fan-favourite and Weir was a central part of the team's dynamic and half of a Fan-Preferred Couple. Weir's successors Carter and Woolsey never really fitted with the rest of the characters, (Carter turning into a Weir stand-in rather than her beloved SG-1 character) while Keller was seen as a Replacement Scrappy. Then you've got Teyla's pregnancy, relationship with Kanaan and the Athosian's disappearance which had potential but never developed properly, the Ronon/Keller/Mckay Love Triangle that quickly morphed into an unpopular Keller/Mckay relationship and nonsensical Season 5 finale. About the only good part was Todd.
Senseless Sacrifice: Beckett's refusal to abandon his patient (who had a tumor that would explode like a bomb at any moment) saves the patient, but gets both Beckett and the EOD technician he was handing the bomb off to killed when it blows up. There would've been one less fatality if he'd just done as Sheppard ordered and left the guy.
Shipping: A lot of it, with Teyla/Kanaan, Ronon/Amelia and McKay/Keller all now canon. (Although most fans weren't happy about the last one.)
As indicated above, the largest slash ship in the fandom is John Sheppard/Rodney McKay and the largest straight ship is John/Weir. But John/Ronon, Rodney/Weir and Ronon/Teyla also have their fanbases.
Both John/Elizabeth and John/Teyla. He has kissed both women at different times and have share quiet moments with them, but usually through some sort of plot device instead of actual romantic feelings. The Legacy series of spin-off novels still enjoy teasing the John/Teyla angle, but the novels' canonicity is dubious. John/Elizabeth was helped by the actors playing them from a romantic angle and John remaining single after her death (Which the still-outraged Elizabeth fans aren't slow to point out).
Ronon/Teyla was the biggest tease for Teyla after Season 1, although it was toned down when Kanaan/Teyla became canon.
Ronon/Keller before deciding to go the McKay/Keller route.
Kavanagh in 38 Minutes. His concern about the danger of the Jumper fragments killing people may well have been reasonable. Weir had no basis for thinking it wasn't other than the fact that the other scientists regarded it as a remote possibility. Yet, when he responded by acknowledging that he at least had to point it out (and without him having pushed the issue any further than that), it was actually Weir who wasted the time of the team by taking the time out of her schedule to undercut and humiliate him in front of his people. In fact, there was no indication that if Weir has simply treated his opinion like a valid scientific consideration rather than the ravings of a coward that he'd have had a problem with it. He was wrong to waste the time calling her out for her behaviour when he did, but her behaviour was also wrong. Yet the fact that he's a jerk meant that his point about her behaviour was treated as automatically wrong, rather that simply his timing in reacting to her behaviour.
Except that she didn't humiliate - at worst, she was brusque, and he then went on to whine about how she'd bruised his ego, trying a power play when the clock was ticking.
Michael points out the considering the Atlantis expedition's treatment of not only him but anything that isn't human or is a threat, they are incredibly similar to the Wraith. The fact is, he's right. If the Atlantis expedition had been the bad guys, their behaviour would have put them beyond the Moral Event Horizon.
However, John's 'alliance' with Todd went a long way to helping to get back to moral ground, showing that yes, Michael was right, but being incredibly similar to the Wraith isn't always a bad thing. Remember, the only thing the Wraith can feed on is humans. They aren't the Goa'uld.
Furthermore, as several Wraith characters point out, it's not as if they have a choice in feeding. While they do possess a digestive tract and are capable of eating regular food, they lose the ability to gain any nutrients or sustenance from it during adolescence, when their need to feed on humans first manifests. Ultimately, the Wraith are just as much victims of their own biology, as the humans they prey upon, although their culture which celebrates the feeding process is something we could have definitely gone without.
At some point in the series they have a Wraith describe what it's like to go without feeding for any extended period of time (getting less "food" than they need). Once they hit their equivalent of puberty, their digestive system shuts down, and feeding on humans is the only way they can survive. It's described as a burning hunger that makes them feel like they're on fire inside. It *literally* hurts like hell, and eventually drives them crazy, shortly before they die of starvation.
It would also have helped their case a bit if they'd been shown to make more of an effort to find some substitute for feeding on humans. They'd been technologically advanced enough to fight the Ancients a very long time ago; they should have been able to come up with some form of "I Can't Believe It's Not Human" by now. Potentially they could even have genetically engineered some non-intelligent humanoid life form capable of sustaining them and lived in peace with the humans.
Teyla, particularly in Season 4. Her people have been on the run from life-sucking aliens for as long as she can remember, both her parents are dead and her partner and all her people get taken just after she discovers she's pregnant.
John: A self-loathing Broken Ace, estranged from his family and carrying a horrible Guilt Complex. Pre-Atlantis he lost numerous friends despite trying desperately hard to save them which the military hate him for and basically kicked him to the curb. He's dedicated to Atlantis because it's people are basically the only thing he's got in life and several sub-conscious hallucinations show he's still hates himself for every past failures and deep down believes he deserves to suffer.
Elizabeth fares better than a lot of the crew, but she still goes through the wringer between her fiancee back on Earth finding someone else, repeatedly sending her team into danger while stuck behind and making more than one Sadistic Choice concerning her closest friend's life.
McKay, too, though his tend to be of the Butt-Monkey variety. He was once caught in a machine that nearly forced him to ascend or die. He developed the Pegusus version of Alzheimer's Disease, which again nearly killed him. In the first season, he was tortured for information.
Stoic Woobie: Ronan. His whole planet was wiped out, his wife was killed and he spent years running for his life being used as a play-toy for wraith, unable to get close to anyone.
Woobie, Destroyer of Worlds: Poor, poor Michael... at least in his first episode. After a while he's just a Jerkass. Well, after the second time Atlantis has betrayed him and tried to kill him.