--> ''Here we are, gloating about the in-fighting among the Wraith. [[NotSoDifferentRemark How are we any different?]]''
---> --- '''Dr. Weir'''

The Atlantis long range scanners pick up a pair of Wraith cruisers headed vaguely in their general direction. Not to worry, they're fighting with each other and not particularly aimed at Atlantis, so one wonders why we even mentioned it. But what's this? We've cut back to the SGC, and it's General Landry, and Major Barrett, and Dr. Lee—heck, even Walter! Basically, every ''[[Series/StargateSG1 SG-1]]'' cast member they can dredge up except the members of SG-1. It turns out that [[TheConspiracy the Trust]] has a (probably human) [[TheMole Mole]] on Atlantis, and the Goa'uld (remember them?) have rigged the city to explode the next time they dial Earth! [[RaceAgainstTheClock Which is later today!]]

Dr. Lee figures out a way to use the ''Daedalus'' and some Stargates to relay a message back to Atlantis, and they shut down the gate and unplug the ZPM just in time. Well, that was easy. And now begin the search for the mole in their midst. Immediate suspicion falls on the [[TheScrappy Dr. Kavanaugh]], currently on board the Daedalus, because, well, he's Kavanaugh (and does in theory have motivation to be a Trust operative). [=McKay=] suspects Lt. Cadman, because he has [[Recap/StargateAtlantisS02E04Duet issues with her]] in general, but nobody pays him any attention. Weir calls Caldwell back to Atlantis and starts interrogating folks. Caldwell calls back to Earth for permission to do so—and then heads back to Atlantis anyway before waiting for a reply.

Unrelated to anything else going on, Teyla's mentor person is in the process of dying of nothing in particular. Dr. Beckett seems to think his hypocratic oath requires him to give her a pacemaker against her express wishes, but comes to his senses eventually. She dies, and the Athosians hold a complicated funeral thing which involves Teyla singing throughout the rest of the drama in the episode.

Such drama comes in the form of the gate up and dialing Earth of its own accord—which fortunately does nothing, since the ZPM is unplugged. While everybody is freaking out over nothing, the distress beacon activates, and the two Wraith cruisers (remember them?) put aside their differences and head over to check it out. Time to cloak up—which requires plugging the ZPM back in, which leaves the city vulnerable to a critical overload if the systems really try—which of course they do. Fortunately, there's a password which will shut everything down. They just need to beat it out of the mole before the ZPM explodes in half an hour from now.

Clearly, the best solution is to start torturing Kavanaugh for information, who has somehow incriminated himself by not having any friends. In case it doesn't work, Caldwell prepares to evacuate everyone to the [[Recap/StargateAtlantisS01E12TheDefiantOne Kill Sat planet]] in the ''Daedalus''. As they are lifting off, Lieutenant Cadman rushes in—she has discovered based on some records anomalies that the mole is in fact [[spoiler: Colonel Caldwell]]—who is a Goa'uld! Good thing they haven't actually started torturing Kavanaugh yet. Sheppard tazes the Goa'uld until [[spoiler: Caldwell]]'s personality resurfaces and reveals the deactivation code. The city is saved (just in time!) and Hermiod gets to work on modifying Asgard beam technology to safely remove the symbiote.

!!Tropes

* AGoodWayToDie: Dying of old age is relatively rare among the Athosians, mostly due to the Wraith. They give special funeral rites called the Ring Ceremony for when it occurs.
* BigLippedAlligatorMoment: Teyla's song might count as one, and the ceremony, particularly given the circumstances, is regarded as something of one InUniverse.
* CharacterOverlap:
** General Landry once again. Dr. Bill Lee also makes his first appearance on the spinoff (and, just as ''SG-1'' did, cements his role as the SGC's secondary scientist whenever Carter's unavailable).
** Downplayed with Malcolm Barrett, who also makes the leap to ''Atlantis''. The NID understandably has no oversight or involvement in the Expedition. Barrett's involvement is only justified due to the then-ongoing Trust investigation on ''SG-1'' and uncovering the intel about the bomb threat. Barrett will only make more appearance on ''Atlantis'' during Season Four.
* ChildHater: Zelenka, played for laughs. The reason he gets sent to [[Recap/StargateAtlantisS01E06ChildhoodsEnd World O’ Children]] is that [=McKay=] is one too, and has slightly more clout.
-->'''Zelenka:''' My sister has a child. He breaks things. He throws things. He smears things onto furniture.
* ColdBloodedTorture: Ronon's plans for Kavanaugh.
* {{Crossover}}: A loose one with ''SG-1'', tying into the parent show's Trust storyline.
* CrazyPrepared: The Trust anticipated their subtle sabotage of Atlantis' power systems might be discovered before the city could be destroyed. So, Caldwell's Goa'uld built in a coded lockout preventing Rodney or anyone else from going into the OS and simply restoring the default settings.
** This also answers why "Caldwell" didn't overtly try to sabotage the messaging efforts earlier. He knew it would draw attention, plus the Trust had contingencies built into the plan that could be activated.
* CustomUniformOfSexy: Lt. Cadman's hair. As a Marine, it should be short (like Carter's) or tied up (like in "Duet") while she's on duty—but it's just not.
** Acknowledged in the audio commentary for exactly this trope: she's sexier with her hair down.
** Although, when Carter takes over as head of Atlantis in season 4, she has long hair (guess Amanda Tapping finally put her foot down.) It is HandWaved as a result of more lax military protocol on the base (given the whole "other galaxy, not terribly accountable to anyone" thing.)
** IRL, it's because the Air Force was not a consultant for Atlantis. They enforced the hair on Carter's character as long as they had approval over it on [=SG1=]. At some point during the making of Atlantis, some AF pilots offered the actor who played Sheppard a ride in one of their shiny planes if he got his famously messy hair cut to regulation length. The producers (ironically, the same producers who wouldn't let Jason Momoa cut off Ronon's signature dreads) wouldn't let him.
* DidntSeeThatComing: In the climax, the Expedition believed that [[spoiler: Caldwell]] was working for the Goa'uld. They didn't anticipate that [[spoiler: Caldwell ''was'' a Goa'uld.]]
** It can arguably be justified in-universe. [[spoiler: The SGC at this point's had almost a decade to spot and deal with Goa'uld infiltration. With all the scrutiny surrounding the Atlantis Expedition and the BC-304s, the odds of a Goa'uld-controlled host actually getting that far undetected should have been all but impossible.]]
* DistressCall: Used to attract the Wraith to Atlantis; [=McKay=] responds with a fake distress call attached to a bit of charred rubble to not give away their continued existence.
* EnemyCivilWar: The Wraith are divided into different factions which have started fighting each other over limited food sources.
* EnemyMine: Among the bad guys, oddly enough. Atlantis picks up two Wraith cruisers in the vicinity who are in the middle of fighting each other; when the distress signal goes up, they promptly stop shooting and join forces to investigate. Probably justified because the main thing the Wraith fight over is feeding grounds; since Atlantis represents a way to get to a whole new massive untouched feeding ground, the chance of finding it is worth a lot more than continuing the fight.
* EveryoneHasStandards: Subverted. Only Rodney seems disturbed at the idea of torturing Kavanaugh. [[spoiler: In the end, they don't actually go through with it, instead faking it.]] Everyone else present, including Shepard and Weir, barely show much in the way of restraint, though Weir later shows a significant degree of disquiet at how quickly everyone, including her, was willing to cross that line.
* ExactTimeToFailure: seems averted at first, when [=McKay=] gives a ballpark estimate of “we have maybe half an hour”—then played straight as all of his subsequent numbers are impossibly precise.
* FaintInShock: Kavanaugh faints at the prospect of his impending torture.
* GlowingEyesOfDoom: The classic Goa'uld eye-flash proving that they are right about [[spoiler: Caldwell]]
* GoingCritical
* GreaterScopeVillain: Ba'al. While he doesn't appear (and isn't even technically mentioned), he's now in control of the Trust thanks to events over on ''SG-1''. So, the order to destroy Atlantis rather than acquire its technology for the Goa'uld would've been given by him.
* IntersceneDiegetic: Teyla's song is heard while the rest of the base prepares to evacuate.
* InternalReveal: Minor one. Ronan learns of the Goa'uld.
* MeaningfulFuneral: Among the Athosians, it is considered a rare blessing to die of natural causes. The Ring Ceremony celebrates this while honoring the deceased. The Expedition are largely puzzled by this, and considering the inconvenient timing, somewhat reluctant to put up with the distraction.
* NeverMyFault: Kavanaugh complains he left the Expedition following "The Siege" because of working conditions. He didn't feel welcome at the City or that his work was appreciated. Yet, it was his own attitude problems during Season One that made him unpopular (and trying to throw Weir under the bus during "Letters from Pegasus" also didn't help his standing either).
* [[NotHimself Not Themself]]: It's a bit surprising that even [[spoiler: Caldwell]] is okay with the idea of torture—until it turns out to be on account of being a Goa'uld at the time.
* OhCrap: Rodney and Sheppard's reactions to learning they're not just dealing with the Trust, but also with the Goa'uld as well. Sheppard by now's read enough SGC mission reports to be familiar with the Stargate Program's oldest foe, while Rodney of course has personal experience with the Goa'uld thanks to the events of "48 Hours" and especially "Redemption Parts 1 & 2".
* OOCIsSeriousBusiness: The Goa'uld would rather blow up Atlantis (to prevent the Wraith from making a grab at the Milky Way) than try to steal its advanced technology for themselves.
* OutsideContextProblem: Zigzagged with the Goa'uld in this episode. The Goa'uld are certainly this for Ronon, as he's used to dealing with the Wraith instead of a PuppeteerParasite. While the SGC has had extensive experience against the Goa'uld after a decade at this point, the Expedition itself is also understandably more experienced dealing with the Wraith on a day-to-day basis.
* PopculturalOsmosisFailure: Dr. Lee is the only person who knows what he's talking about when he compares the relay setup to [[WesternAnimation/OneHundredAndOneDalmatians the Twilight Bark]]; when he changes the analogy to [[Film/TheLordOfTheRings Lord of the Rings]], the rest of the room immediately starts nodding.
* RedHerringMole: Dr. Kavanaugh looks pretty suspicious—until you realize that's how he acts ''all the time.''
* RequiredSpinoffCrossover: With contact with Earth re-established at the beginning of the Season, the Goa'uld make their first and only appearance outside of ''Series/StargateSG1'' (at least in the Brad Wright-era canon if you're counting ''Series/StargateOrigins''). This one at least is justified with the Trust then-active on the parent show and the need to address why the Goa'uld would or wouldn't be trying to get their hands on the advanced Ancient technology of the Pegasus Galaxy.
* RewatchBonus: Played straight with Caldwell's scenes in this episode after the Goa'uld reveal. However, it's ''also'' subverted with his previous Season Two appearances, because it's never revealed ''when'' the Trust implanted the Goa'uld in Caldwell's head. It could have been there as early as "The Siege, Part III", or at the very least just prior to this episode. The closest we ever get to an answer is that the post-Goa'uld Cadlwell is friendlier and on much better terms with the Expedition for the remainder of the series.
* TheCastShowoff: Yeah, that's actually Creator/RachelLuttrell singing there.
* TheMole: [[spoiler: Col. Caldwell]].
* ThrowTheDogABone: Dr. Lee manages to be the one to save the day, at least at first, when he figures out a way to relay a message to Atlantis via the ''Daedalus''.
* TheUnreveal: Again, it's left unrevealed ''when'' the Trust put the Goa'uld inside Caldwell (if it was immediately prior to this episode, or as far back as the Season Premiere).
* WeaponizedTeleportation: Apparently the Asgard can just beam Goa'uld symbiotes out of people... albeit once the beam is modified. Possibly Justified by contact between the Asgard and the Tok'ra (who can remove symbiotes) via Earth humans.
* WhamShot: See Glowing Eyes of Doom.
----