* AcceptableHardLuckTargets: Dr. [=McKay's=] allergies and hypoglycemia.
* AcceptableTargets: Sheppard frequently excuses Rodney to people because... "He's Canadian"
** Kavanagh, described by the producers as the most irritating person in 3 galaxies.
--> '''Hermiod''': Doctor Kavanagh?
--> '''Kavanagh''': Yes?
--> '''Hermiod''': Stop... talking... please... *{{Beat}}* Thank you.
* AccidentalInnuendo:
** Jack O'Neill assures Dr. Weir that she and her team will remain in Atlantis as, in his words:
-->'''O'Neill''': Since you saved Woolsey's ass, and you did a fair job on mine...
** This exchange from 5.15 'Remnants', as Richard Woolsey sees that a women he's been flirting with found his balcony hang-out spot:
-->'''Woolsey''': You’ve approached my private spot!
-->'''Woman''': ...What?
-->'''Woolsey''': [[DiggingYourselfDeeper I mean you’ve entered my little personal area]].
-->[{{Beat}}]
-->'''Woolsey''': ...This is where I come... to be alone with my thoughts.
* AlternativeCharacterInterpretation: The main cast: [[BigDamnHeroes big damn heroes adventuring and exploring new worlds while trying to make it in the Pegasus galaxy]], [[DesignatedHero malicious idiots that leave a trail of death, destruction and imminent doom everywhere they go]] or [[BlackandGreyMorality humanity's ruthless defense against a new intergalactic, genocidal threat]]?
** Or a combination of all 3.
** Dr. Kavanaugh: StrawmanHasAPoint or TheComplainerIsAlwaysWrong?
** Elizabeth Weir: [[GuileHero a gifted negotiator who fights hard for her people's freedom in the face of nigh insurmountable odds]] or a ManipulativeBitch who bullies and threatens other cultures and people for the betterment of her own, [[MoralDissonance judging them by a morality that is convenient to her]] in order to justify her actions?
*** Keeping in mind the number of times she's used ultimatums as a negotiating strategy
* AssPull: [[spoiler: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 [[ChekhovsGun Chekhov's Gun]] out of their ass.
* BaseBreaker: Rodney [=McKay=]. You either like that the smart guy is the one who saves the day or find him incredibly grating.
* CrowningMusicOfAwesome: From the season 2 episode "Critical Mass": [[http://www.youtube.com/watch?v=WESoHaRkJSo "Beyond The Night"]]. Oh, and that IS [[TheCastShowoff Rachel Luttrell]].
** From "Rising" we have [[http://www.youtube.com/watch?v=v57ID1sHeOk&list=PLD09FF0FC42951062 "Gate to Atlantis"]], [[http://www.youtube.com/watch?v=YcEozKGWjRc&list=PLD09FF0FC42951062 "The Rescue"]] and [[http://www.youtube.com/watch?v=TYiKW1fnBKQ&list=PLD09FF0FC42951062 "Our New Home, Atlantis"]]. All of which are designed to fill you with a sense of adventure.
* CrowningMomentOfFunny: 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!"
* DamselScrappy: Dr Keller
* DesignatedHero: although our heroes are in general good guys, there are some episodes where what they do is at the least soaked in MoralDissonance and at the most downright evil. In "Infection" where Sheppard comes across 'Todd's diseased Wraith hive ship where his entire crew - now having undergone a gene therapy where they can no longer feed - are in stasis pods. However, because of the ship's malfunctions there is an off-chance that they might break free from the pods and attack Sheppard's team and the team of marines - all of whom are heavily armed against Wraith who are sick and dying. 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. When we don't have a clear answer as to "whose actions are more amoral, the heroes or Todd?" there's a bit of a problem.
* DesignatedVillain: Bates, Kavanaugh and Ellis tend to end up in this role. [[StrawmanHasAPoint They usually have legitimate concerns or complaints]], but because these are against the main cast of characters (Bates seeing Teyla as a security risk, Kavanaugh complaining to Weir about Weir dismissing his concerns, Ellis wanting [=McKay=] to cut the exposition and get to the point) the characters are presented as reactionary jerkasses. 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.
** Ellis isn't so much a DesignatedVillain as a JerkAss who likes to bully and harass those who make him feel inferior. He's a good man 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 (not that Sam is a mean person or anything, but she wouldn't defend Rodney like that unless what Ellis was saying was absolutely unacceptable, particularly considering that he's of equal rank).
* DieForOurShip: Keller gets this a lot.
** When fans are in a more forgiving mood, she often gets [[ShipTease paired with]] [[FanPreferredCouple Ronon]].
* DracoInLeatherPants:
** Michael is a subject of some contention with this trope. Many people express their disapproval on how Michael is treated. It's easy to think that all this "Kill almost everybody and turn the rest into unstoppable army of destruction" kinda slips their mind. That said, disapproval of his treatment doesn't mean approval of his actions - just because the enemy is evil, it doesn't mean the heroes get a free pass to go play at the MoralEventHorizon. 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 OmnicidalManiac who would use a baby to perfect his mindless army, no matter what made him that way.
** You wouldn't believe how many {{fangirl}}s Todd has.
* EngagingChevrons: 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''.
* EnsembleDarkhorse
** Doctors Carson Beckett and Radek Zelenka!
** 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 SureWhyNot and made it onto the show.
** Todd the Wraith.
* FanPreferredCouple: 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.
* FridgeHorror: 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 [[{{ArchEnemy}} 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 HappilyEverAfter).
* GeniusBonus: Genii is the plural form the Latin word "Genius" (no pun intended).
* GrowingTheBeard: All the {{Badass}} characters either show up or are promoted in season 2: Ronon, Caldwell, Lorne, Sheppard, etc.
* HilariousInHindsight: In "Epiphany", [=McKay=] refers to Ronon and Teyla as "[[Franchise/ConanTheBarbarian Conan]] and [[Series/XenaWarriorPrincess Xena]]". Jason Momoa would later go on to play Conan himself in the [[Film/ConanTheBarbarian2011 2011 film reboot]].
* HoYay: Lets see;
** Sheppard and [=McKay=] are everyone's favorites with scenes that seems to back it up (the end of Irresistible for expamle).
** Beckett and [=McKay=] are great friends and even kissed once while [=McKay=] was sharing a body with the mind of a female soldier.
** A FoeYay 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.
* HoYayShipping: Most notably, John Sheppard and Rodney [=McKay=]. There are some people who watch the show ''specifically because of this''.
* IdiotPlot: The whole SeriesFinale.
** 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 [[WhatTheHellHero betrays him again]]. [[TooDumbToLive 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.
* JerkassWoobie: 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 recieved 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 Altarens decided that they were NotEvenHuman 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 AbusiveParents.
** 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.
* LauncherOfAThousandShips: [=McKay=].
* MagnificentBastard: The Wraith "Todd" lives this as a matter of course; manipulating enemies with style is like breathing to him.
** Major Sheppard also gets a moment like this every so often, including and especially at the end of the series, when he's trying to talk "Todd" into helping them fight another Wraith. "Todd" asks Sheppard why he should do it when it would leave "Todd" the prisoner of Atlantis and without any leverage.
--> Todd: Am I supposed to be enticed by this offer?
--> Sheppard: No. I'll probably kill you anyway. But don't forget, this Wraith betrayed you and got away with it. For no other reason, you might want to do it out of pure spite.
--> Todd: ''Youuuu know how to talk to me'', John Sheppard! (evil laughter)
* MemeticMutation: [=McKay=]'s [[PlotAllergy citrus allergy]].
* MoralEventHorizon: 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 AndIMustScream 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 [[NeglectfulPrecursors some of their messes]], we didn't mean through ''[[KillItWithFire carpet-bombing!]]''
* NightmareFuel: The hallucinations in the season 1 episode "Hot Zone", caused by an [[spoiler: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 [[spoiler: Kate Heightmeyer]] and provides no real reason for it's actions other than ItAmusedMe. 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.
* ReplacementScrappy: Keller to a certain extent, partly because of what happened to Beckett.
* {{Shipping}}: A lot of it, with Teyla/Kanaan, Ronon/Amelia and [=McKay=]×Keller all now canon. (Although most fans were not happy about the last one).
** As indicated above, the largest slash ship in the fandom is John Sheppard/Rodney [=McKay=], although there is a decent portion that also enjoy seeing John/Ronon and Ronon/Rodney.
** John/Elizabeth and John/Teyla were both ShipTeased. 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.
** The John/Teyla ship was also neglected in later series as Ronon/Teyla was introduced and Kanaan/Teyla became canon. However the most popular straight pairing is still John/Elizabeth, especially as John remained single after her death (her death itself caused outrage among the fans).
** The writers also {{Ship Tease}}d Ronon/Keller before deciding to go the [=McKay=]/Keller route, which the fandom reacted much more positively to (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).
* StrawmanHasAPoint: 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 behavior would have put them beyond the MoralEventHorizon.
** 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 [[AlwaysChaoticEvil the Goa'uld]].
** Furthermore, as several Wraith characters point out, it's not as if they have a ''[[HorrorHunger 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.
* UnfortunateImplications: Lucius Lavin in "Irresistible" essentially roofied an entire village and Atlantis into being his adoring public, date-raped numerous women and is [[KarmaHoudini not punished]] in the slightest for his actions. Instead, it's PlayedForLaughs.
*** He gets sent back to the planet after the people are immune to his charms. The implication is that he'll be plenty punished by the outraged villagers he manipulated.
** We do find out later in "Irresponsible" that his wives divorced him and he was banished from the village, but even so, he seems to have been [[KarmaHoudini let off the hook]] rather easily. Furthermore, he doesn't appear to have [[AesopAmnesia learned a thing]] about why it's wrong to manipulate people, since he's right back at it in the latter episode!
* UnpopularPopularCharacter: Most of Atlantis treats Zelenka this way.
* VillainDecay: The Wraith seem to go through this, especially in the last couple of seasons, due to both LoweredMonsterDifficulty and the story changing the emphasis from "the Wraith slowly wiping out all Pegasus humans" to battles against EvilerThanThou enemies such as the Replicators and Michael.
** Todd also helped with the VillainDecay, because he gave a lot of insight into Wraith culture, and someone decided not to make them as evil as we were first led to believe.
* VisualEffectsOfAwesome: Considering the typical production values of an average sci-fi TV series, the series has amazing CGI effects. Most prominent in "The Siege" three-parter episode.
* WhatMeasureIsANonBadass: Keller.
* TheWoobie: 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.
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