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{{quote|''"[[To Serve Man|We don't require our food to agree with us.]]"''|'''Wraith Queen'''}}
 
'''''Stargate Atlantis''''' is a spin-off of the popular sci-fi show ''[[Stargate SG-1 (TV)|Stargate SG-1]]''.
 
SG-1 spent its seventh season searching for a "lost city", which they believed was actually [[Ancient Astronauts|a ship]] belonging to the [[Precursors|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 ''[[Stargate SG-1 (TV)|Stargate 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 ''[[Stargate SG-1 (TV)|Stargate SG-1]]'' after the first episode of season eight, and continues for five seasons. It is currently set to continue through a series of tie-in novels.
 
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{{quote| '''Dr. Jennifer Keller:''' Seriously, have you tried these strawberries?}}
* [[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 (TV)|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.
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* [[As You Know]]: When Woolsey tries it with Ronon, [[Subverted Trope|Ronon says that he actually did not know that]]. [[Double Subverted|Woolsey follows up that he previously explained it personally]], [[Zig Zagged Trope|but Ronon says he missed that meeting, and Woolsey says that]] ''[[Zig Zagged Trope|he saw Ronon there]]''.
* [[Atlantis]]: In this series, it's an ancient city-cized spaceship, rather than an ancient mythical continent.
* [[Back for Thethe Dead]]: Lt. Ford is first [[Put Onon a Bus]], brought back, then [[Put Onon 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]]: {{spoiler|Carson Beckett, who dies at the end of season three and returns at the end of season four [[Send in Thethe Clones|in clone form]].}}
* [[Badass Abnormal]]: 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. [[With Great Power Comes Great Insanity|Too bad it also drove him insane]].
* [[Badass in Aa 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.
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* [[Bare Your Midriff]]: Teyla in most of her "civilian" clothes.
* [[Bash Brothers]]: Ronon and Teal'c... versus the Wraith.
* [[Battle in Thethe Center of Thethe Mind]]: The entirety of "The Real World."
* [[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 [[Barely-There Swimwear|tiny bikini]] and Elizabeth would be dressed in an [[Old-Timey Bathing Suit|all-concealing parka.]]
* [[Beneficial Disease]]:
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* [[Bury Your Gays]]: The only Atlantis personnel to die in "Whispers" is Captain Vega, who had been implied (In [[Hide Your Lesbians|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 "[[Spock Speak|undomesticated equines]]" (Wild Horses) could not keep him from visiting her. She laughs and [[Lampshade Hanging|says]] "nice [[Call Back]];" Teal'c had first referred to horses in such a manner back in season one of ''[[Stargate SG-1 (TV)|Stargate SG-1]]''.
* [[Captain Smooth and Sergeant Rough]]: Major Sheppard and Sergeant Bates in the first season. Bates, a [[Semper Fi|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.
* [[The Cast Showoff]]: Yes, that really is Rachel Luttrell singing in the episode "Critical Mass".
* [[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 Withwith 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 [[Semper Fi|US Marines]] arrive to defend Atlantis from Wraith attack, and then the USS ''Daedalus'' arrives [[Gunship Rescue|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 Moments]] when Rodney asks Neil deGrasse Tyson [[Pluto Is Expendable|if he has made any children cry today]].
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* [[Conflict Killer]]: Teyla and Sergant Bates had 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 exchanged physical blows after Bates made an explicit accusation after a mission went wrong. {{spoiler|Later in the episode Bates was discovered beaten so severely that Beckett felt it was 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 was shipped out of the base for treatment and never returned to Atlantis}}.
* [[Continuity Porn]]: In "''Doppplerganger''", 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''".
* [[Cool Gate]]: It is ''Star'''[[Exactly What It Says Onon the Tin|gate]]''' 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 charactes 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."
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* [[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. [[Never Heard That One Before|Zelenka explains how that never gets old]].
* [[Development Hell]]: Production for the direct to DVD film ''Extinction'' has been put on hold indefinitely due to the cancellation of ''[[Stargate Universe (TV)|Stargate Universe]]''.
* [[Die Hard Onon an X]]: "The Prodigal". The episode even ends with Teyla tossing <s>Hans Gruber</s> {{spoiler|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 Carter points out that if Keller 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.
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** 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 beam him into outer space, with the episode closing on a shot of him floating around.
** The second is of {{spoiler|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 Onon the Reich]].
* [[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.
* [[Early-Bird Cameo]]: ''SG-1'''s "Merlin" slips in an appearance before he is even alluded to on the mothership show.
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* [[Enemy Mine]]: "Common Ground," the introductory episode of Todd the Wraith, featured 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.
* [[Establishing Character Moment]]:
** Before you knew his name you only knew Sheppard as the one to save [[Stargate SG-1 (TV)|Jack O'Neill's]] life from a wayward Ancient attack drone.
** Ronon's introductory episode has him getting into a fistfight with Ford (who was inhumanly strong [[With Great Power Comes Great Insanity|and crazy]] because of a [[Psycho Serum]] accident) and not only matching him in combat, but seemed 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 [[Replacement Flat Character|less cooperative and used to the Pegasus galaxy than Colonel Caldwell]].
* [[Everything's Better Withwith Spinning]]: Subverted: The symbol ring on the Pegasus gates are stationary and the illuminated panels simply give the ''illusion'' of spinning.
* [[Evil Is Visceral]]: The Wraith use [[Organic Technology]] and are not very pretty themselves.
* [[Expy]]:
** Ronon to Tyr Anasazi from ''[[Andromeda]]''.
** Beckett to [[Star Trek: theThe Original Series|Dr. McCoy]]. Sheppard even goes so far as to describe McCoy as "the TV character Dr. Beckett [[This Is Reality|plays in real life]]."
* [[Face Death Withwith Dignity]]: Colonel Marshall Sumner, [[Semper Fi|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]]: {{spoiler|Otho}} towards the conclusion of "The Tower."
* [[Fake American]]: Most of the main cast are Canadians playing Americans. In the original cast, only Joe Flanigan (American playing an American) and David Hewlett (Canadian playing a Canadian) were actually playing their correct nationalities. They are, by coincidence, also the only characters to appear in every episode of the series.
* [[Fake Nationality]]: [[Playing Withwith a Trope|Sort of]]. Many of the actors were born in the countries that their characters are from, but they emigrated to Canada at young ages.
** Zelenka. David Nykl was born in the Czech Republic, but having lived most of his life in Canada he is not using his normal accent.
** Paul McGillion (Carson Beckett); born in Scotland, grew up in Canada, and has spent time back and forth.
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** Zelenka is known to rant in Czech when frustrated.
** Hermiod frequently complains about humanity in Asgard, which is actually just English in reverse.
* [[Geeky Turn On]]: Dr. Weir distracts a scientist by talking about ''[[World of Warcraft (Video Game)|World of Warcraft]]''. Incompetently.
* [[Genre Savvy]]: Sheppard repeatedly show an awareness of sci-fi cliches and what roles they play, that Ronon is "Chewie" and Beckett is "McCoy".
* [[Get Back to Thethe Future]]: "Before I Sleep" exists at the nexus of this trope, [[Trapped in Thethe Past]], and [[The Slow Path]].
* [[Get It Over With]]: The third-season episode 'Common Ground', where the Wraith [[Magnificent Bastard|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. {{spoiler|Then Todd gives back all the life-energy he took from him because he helped him escape from a Genii prison.}}
{{quote| '''Sheppard''': Finish it.<br />
'''Todd''': As I told you, John Sheppard, there are many things about Wraith that you do not know. }}
* [[Go-Karting Withwith 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 [[Useful Notes/Mensa|Mensa]]-worthy IQ.
* [[Good News, Bad News]]:
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{{quote| '''{{spoiler|Caldwell}}:''' "I warn you as a Go'uld I possess the strength of many men."<br />
'''Ronon:''' "Then it'll be a fair fight." }}
* [[I'm a Doctor, Not Aa Placeholder]]: Carson often in season 1, specifically in "The Brotherhood".
** "For the last time, I'm a doctor, not a bloody fighter pilot!"
** "I'm a bloody medical doctor, not a magician!"
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'''Hermiod''': Shut... up... 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.
* [[Jerk Withwith 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 [[Love Triangle|Rodney]] ''[[Love Triangle|or]]'' [[Love Triangle|Ronon.]]
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* [[Mama Bear]]: Teyla. Threaten her child, {{spoiler|get thrown off a skyscraper}}.
* [[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. {{spoiler|Too bad she is a mental projection from an AI that was created after gleaning his romantic and sexual desires from his mind}}.
* [[Married to Thethe Job]]: The reason Sheppard and his ex-wife Nancy divorced was because 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.
* [[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 (TV)|Stargate SG-1]]'', but it was never confirmed if it was the same character [[You Look Familiar|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 [[The Danza|called him by the actor's first name]] [[Sure Why Not|and that was kept in the show]]. He recurred until the finale as one of Atlantis's operators and technicians.
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* [[Multitasked Conversation]]: When Woolsey is seeing the mental projection of an AI 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 AI at the same time he tries to pretend that his (Almost panicked) dialogue with the AI 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 [[The War Onon Terror|Afghanistan]]. {{spoiler|He did not make it}}.
** Ronon blames himself for bringing the Wraith to a village where he once spent the night when he was Runner.
** McKay destroyed [[Insistent Terminology|5/6]] of a solar system when he let his hubris get the better of his judgement.
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* [[Never Heard That One Before]]: When Zelenka tells Elizabeth that the Ancient computer system is incredibly redundant, Elizabeth [[Department of Redundancy Department|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 feed on many humans. They created Michael, who killed many humans, quite a few of them by using the Hoffan drug that the Atlantis team helped develop three seasons earlier. They reprogrammed the Asurans to attack the Wraith... who did so by killing humans (their food). Finally, they gave the Lost Tribe the means to defeat the Wraith which - you guessed it - caused the deaths of many of humans. In other words, they are basically responsible for almost every recurring villain in the show.
* [[Nice to Thethe Waiter]]: Woolsey attempts to show the IOA 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 "[[Hey, You|you]]".
* [[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 [[Berserk Button|insults Ronon's Satedan history]] and drives Ronon to draw his gun; [[Ironic Echo|which of course he would never do, since he knows how to play the game]].
* [[Not That Kind of Doctor]]: McKay
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** 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.
* [[One-Man Army]]: Ronon in "''Sateda''" where he single-handedly takes down multiple Wraith platoons in the ruins of his homeworld.
* [[Only Known Byby Their Nickname]]: 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".
* [[Organic Technology]]: The Wraith.
* [[Other Me Annoys Me]] In one episode, an alternate universe version of Rodney McKay appears. This version is charming, extroverted and socially skilled. The regular Rodney ends up disliking him because everyone seems to like him better.
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* [[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.
* [[Plot Tailored to Thethe Party]]: [[Inverted Trope|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.
* [[Portal Slam]]: Like ''[[Stargate SG-1 (TV)|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.
* [[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, [[Getting Crap Past the Radar|in contravention of SyFy's censorship standards, to boot]].
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** 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.
* [[Puppeteer Parasite]]: In ''Critical Mass'', it is revealed that {{spoiler|Colonel Caldwell}} has become host to a Goa'uld in the employ of one of the ''[[Stargate SG -1]]'' villains.
* [[Putting Onon 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.
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* [[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 Subtext]]:
** When Col. Samantha Carter leaves [[Stargate SG-1 (TV)|SG-1]] to [[Transplant|become leader of the Atlantis Expedition]], she says, "I know I am going to miss this place, and all of you," to old friend Teal'c. The tears in [[Amanda Tapping]]'s eyes were likely not faked; she herself was saying goodbye to ''SG-1'' after ten years.
** Jason Momoa got a large tattoo on his left forearm between the filming of seasons two and three, forcing Ronon to likewise get a tattoo in the series. This was applied in "Reunion," where the application apparently hurt and forced Ronon to lightly slap the person doing the inking; Jason had not told the producers about the tattoo, and they were unhappy to learn about it after the fact.
** Teyla became pregnant in the fourth season when Rachel Luttrell became pregnant in real life.
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** The first season episode "Home." {{spoiler|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.
* [[Seinfeldian Conversation]]: When they are trapped in a Puddle Jumper and awaiting rescue, doctors Lee and Cavanaugh spiritedly discuss the merits of [[Michael Bay]]'s ''[[Pearl Harbor]]''. Lee is disdainful of the project, but Cavanaugh believes that the film has "weight" and will [[Vindicated Byby History|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 Thethe Clones]]: {{spoiler|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.
* [[Shout-Out]]:
** 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 "[[Jaws (Filmfilm)|We're gonna need a bigger boat.]]"
** In "The Defiant One" Rodney calls Sheppard "[[Star Trek|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 [[Boldly Coming|gets involved with alien women]].
** A frustrated Rodney once refers to Ronon and Teyla as ''[[Conan]]'' and ''[[Xena]]''
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[[Beat Panel|Beat]]<br />
'''John Sheppard''': "Now!" }}
** 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 [[The Terminator|vat of molten lead]] or [[The Lord of the Rings (Filmfilm)|a volcano]]. This, of course, [[Eureka Moment|gave Sheppard an idea]].
** Part of Rodney's long numerical computer password, as revealed in season four's "Quarantine," is [[The HitchhikersHitchhiker's Guide to Thethe Galaxy|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 [[Theme Music Power-Up|Batman theme music]] subtly plays as he pulls himself onto a ledge.
** In "The Hive," Sheppard is talking to a fellow prisoner, Neera {{spoiler|who turns out to be a Wraith-worshipper placed there to pump Sheppard for information}}, and mentions his [[wikipedia:Coulrophobia|fear of clowns]].
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* [[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, Hero?|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.
* [[Throw It In]]: After Torri Higginson accidentally called the Gate Technician by his real name, "Chuck", the producers decided to keep it in and make it has official name, since he had not had one until that point.
* [[Tomato in Thethe Mirror]]:
** The titular character in "''Michael''" realising that he is not a human with amnesia, but he is actually a ''Wraith''.
** Halfway through "This Mortal Coil" {{spoiler|the primary cast discovers that they are all Replicator-built ''copies'' of the Atlantis staff.}}
* [[Too Clever Byby Half]]: McKay
* [[Took a Level In Jerkass]]: The Vanir {{spoiler|Asgard}} who are incredibly ruthless compared to {{spoiler|their Ida Galaxy cousins}}.
* [[Touched Byby Vorlons]]: {{spoiler|Elizabeth Weir becomes a Replicator.}}
* [[Transplant]]:
** 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 [[You Look Familiar|having him play a new character]].
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** Both the Wraith and the humans of the Altantis expedition point out that no matter how many Wraith ships they destroy, the Wraith will just send more.
** 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 (TV)|Stargate SG-1]]''.
* [[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 Measure Is a Non-Human?]]:
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** A clip show is actually skillfully done in which the Pegasus Galaxy call the Atlantis Expedition out for all the chaos they have caused.
** "Michael" loves to point this out, that for all their preaching about morality, in regards to torturing and experimenting on prisoners, they violated it several times because of the flimsy justification that human rights do not apply when the enemy ''isn't'' human.
* [[What You Are in Thethe Dark]]: In "Harmony," with the Genii between them an 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.
* [[Wild Card]]: Todd the Wraith, oh so much.
* [[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.
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* [[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. [[Subverted Trope|The subordinate thanks Kolya for his life and goes back to duty, vowing to do better.]] [[Double Subverted|Kolya then turns to another subordinate and orders him to have his gun fixed]].
* [[You Look Familiar]]:
** Craig Veroni, who played Dr. Peter Grodin, first appeared in ''[[Stargate SG-1 (TV)|Stargate SG-1]]'' as an unnamed weapons officer aboard the ''Prometheus'' in the episode "Grace." It was never confirmed if the two were the same character, or if Craig had been re-cast as a different person.
** The Lord Protector from "The Tower" originally appeared twice in ''SG-1'' as Harlan, the amazingly annoying inhabitant of Altair who turned SG-1 into robots.
{{quote| "Komtraya!"}}
** Jewel Staite was a Wraith before she was Dr. Keller. Not very noticeable however, since the Wraith part required full prosphetic make-up that made her virtually unrecognizable.
** In a fairly ludicrous example, an actress in the early episode [[Stargate Atlantis (TV)/Recap/S01 E07 Poisoning the Well|"Poisoning the Well"]] ended up playing the ''exact same role'' to one she did in the ''[[Stargate SG-1 (TV)|Stargate SG-1]]'' episode "Cure" where Tretonin is discovered.
** Christopher Heyerdahl played a character named Pallan on ''SG-1'', and the Athosian Halling on ''Atlantis''. His largest role is the Wraith Todd. At one point he even portrayed both Halling and Todd ''in the same episode'' (without any shared screentime however).
** Paul McGillion, who plays Dr. Carson Beckett, first appeared in the Stargate 'verse as Young Ernest Littlefield in the SG-1 episode "The Torment of Tantalus". Incidentally, he was the first human to travel through Earth's Stargate in modern times.
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