History Recap / StargateAtlantisS02E02TheIntruder

* ContrivedCoincidence: Invoked by Caldwell once Rodney discovers the virus and that it must've been uploaded during "The Siege, Part 3". If it's been in the ship's systems for nearly 2 months, why is it only coming online ''now''? Rodney theorizes it must've been transmitted in a compressed format and was slowly unpacking itself to avoid detection. The virus went dormant after leaving the Pegasus Galaxy and is only come back online now because they're back in proximity to Wraith territory.

* RankUp: Sheppard is promoted from Major to Lt. Colonel.

* HeroAnTagonist: Landry is presented as this here in the context of ''Atlantis'' rather than ''SG-1'' (due to his opposition to Sheppard's continued presence on the Expedition).

* HeroAnagonist: Landry is presented as this here in the context of ''Atlantis'' rather than ''SG-1'' (due to his opposing Sheppard's continued presence on the Expedition).

* ContinuityOverlap: The flashbacks to the SGC and the Expedition's debriefing take place not only after the events of "The Siege, Part 3", but also in-between the ''SG-1'' Season Eight finale "Moebius" and the Season Nine premiere "Avalon, Part 1" (as the ''Daedelus'' was about to undertake the return journey to Pegasus early in that episode). This episode also, again, acknowledges that O'Neill has stepped down as the SGC's commander and that Landry has now succeeded him.

* PassedOverPromotion: Caldwell was the favored candidate to replace the late Colonel Sumner as the Expedition's military commander. He's ''not'' happy that Weir not only went to bat for Sheppard, but won and it's causing friction between him and the Expedition leaders.

* TheReveal: The Wraith covertly uploaded a virus into the ''Daedelus'' systems during "The Siege, Part 3". It's implied it was transmitted by the Wraith Cruiser that was descending and drawing parallel to the BC-304 during the second space battle (based on how that clip's emphasized in the Recap).

** The events of "Critical Mass" later in the Season offer more possible context for his anger. [[spoiler: If Caldwell had the Goa'uld implanted in his head this early in Season Two, commanding the Expedition's military contingent would've given him direct access to the City and its technology -- access he wouldn't have fully had as the ''Daedalus'' commander and his standing orders to assist the Expedition. If this is the case, then Weir unknowingly screwed up those plans.]]

* WholePlotReference: "The Intrudcer" is, for all intents, an ''Atlantis'' remake of [[[[Recap/StargateSG1S4E20Entity "Entity"]] and follows many of the same narrative beats (such as an attempt to wipe the entity failing due to a backup the characters missed). That being said, there are another differences thanks to different storytelling avenues that ''SG-1'' didn't have access to at the time (ex. the BC-304s, the Wraith) to differentiate this episode from its predecessor.

* EurekaMoment: Heimdall's observation that the computer virus is unlike any ''human''-created program he's seen before. This is what gets Rodney to run a Translation Program to confirm or disprove his fears that it's actually a ''Wraith''-created virus.

* CallBack: [=McKay=] compares the situation with the Wraith AI to the similar situation ''SG-1'' experienced 5 years earlier during [[Recap/StargateSG1S4E20Entity "Entity"]].

* CallBack: [=McKay=] compares the situation to the [[Series/StargateSG1 SG-1]] episode "Entity."

* PassedOverPromotion: Caldwell was the favored candidate to replace the late Sumner as the Atlantis Expedition's military commander. He's 'not'' happy that Weir not only went to bat for Sheppard, but won and it causes friction between him and the Expedition leaders.

* PassedOverForPromotion: Caldwell was the favored candidate to replace the late Sumner as the Atlantis Expedition's military commander. He's 'not'' happy that Weir not only went to bat for Sheppard, but won and it causes friction between him and the Expedition leaders.

* PassedOverFoPromotion: Caldwell was the favored candidate to replace the late Sumner as the Atlantis Expedition's military commander. He's 'not'' happy that Weir not only went to bat for Sheppard, but won and it causes friction between him and the Expedition leaders.

* ContinuityOverlap: The flashbacks to the SGC and the Expedition's debriefing take place not only after the events of "The Siege, Part 3", but also in-between the ''SG-1'' Season Eight finale "Moebius" and the Season Nine premiere "Avalon, Part 1" (as the ''Daedelus'' was about to undertake the return journey to Pegasus early in that episode). In the interim between the end of "The Siege, Part 3"). This episode also, again, acknowledges that General O'Neill has stepped down as the SGC's commander and that General Landry has now succeeded him.

* CharacterOverlap: General Hank Landry. Since O'Neill has stepped down from command of the SGC at this point in the timeline (due to RDA leaving ''SG-1 after Season Eight), Landry has succeeded him. As the SGC's new commander, this is the first of several crossover appearances Landry will make on the spinoff show.

* CharacterOverlap: General Hank Landry. Since O'Neill has stepped down from command of the SGC at this point in the timeline (due to RDA leaving ''SG-1 after Season Eight), Landry has now taken command. As the SGC's commander, this is the first of several crossover appearances Landry will make on the spinoff show.

* BothSidesHaveAPoint: Weir and Landry's argument over removing co. Landry is quite correct that as the surviving senior officer after Summner's death in "Rising", he

Hoewever, Weir also rightly argues that Sheppard has left

* PassedOverFoPromotion: Caldwell was the favored candidate to replace Sumner as the Atlantis Expedition's military commander. He's 'not'' happy that Weir not only went to bat for Sheppard,but won and it causes friction between him nad the Expedition leaders.
** The events of "Critical Mass" later in the Season offer more possible context for his anger. [[spoiler: If Caldwell had the Goa'uld implanted in him this early in Season Two, commanding the Expedition's military contingent would've given him direct access to the City and its technology -- access he wouldn't have fully had as the ''Daedelus'' commander and his standing orders to assist the Expedition. Weir going to bat for Sheppard and winning screwed up thos plans.]]

* ContinuityOverlap: The flashbacks to the SGC and the Expedition's debriefing take place not only after the events of "The Siege, Part 3", but also in-between the ''SG-1'' Season Eight finale "Moebius" and the Season Nine premiere "Avalon, Part 1" (as the ''Daedelus'' was about to undertake the return journey to Pegasus early in that episode). In the interim between the end of "The Siege, Part 3"). This episode also acknowledges that General O'Neill has stepped down as the SGC's commander in that interim (due to RDA leaving ''SG-1'') and that General Landry jas now succeeded him.
* EarlyBirdCameo: Since the flashbacks take place prior to "Avalon, Part 1", this episode is the first chronological appearance of Hanky Landry on ''Stargate''.

* YouHadUsWorriedThere: Twice. First after the virus vents the atmosphere in the fighter bay, then again after the battle in the corona of the sun.
* ComputersSpeakBinary: The computer monitor behind Hermiod displays the virus as scrolling columns of zeroes and ones… until they “translate” it into Wraith.

* ExplosiveDecompression: Averted. The poor guy just sort of falls out through the airlock as the pressure equalizes, without any undue windiness or explosion.

* ZeroesAndOnes: The computer monitor behind Hermiod displays the virus as scrolling columns of zeroes and ones… until they “translate” it into Wraith.

Returning to the Pegasus Galaxy from Earth with passel of brand new Atlantis team members, the Daedalus starts experiencing unexpected technical problems. First a scientist is killed by a power surge in a door panel - then another is unexpectedly blown out an airlock. The crew suspect sabotage, and begin searching for an intruder on board.

In fact, the malfunctions are caused by a computer virus - a ''Wraith'' computer virus that they picked up somehow during [[Recap/StargateAtlantisS02E01TheSiegePart3 the battle with several Wraith hive ships.]] It has taken until now (the 18-day trip each way to and from Earth) for it to take over enough of the systems to start causing real problems. In addition to protecting itself, those problems are now taking the form of grabbing hold of the navigational systems to fly the ship straight to the Wraith. In case that doesn't work, it's also sending out a distress signal to call the Wraith to them.

The solution is to reboot the entire ship, then restore the systems from clean back-ups. Unfortunately, the virus is able to hide out in the computers of the F302s in the hangar bays, and re-establishes itself almost instantly. [[FromBadToWorse Worse]], it now has enough control of the Daedalus to direct it to fly into the coronosphere of the local star, which will bake all the people to death while leaving the ship itself largely intact.

[=McKay=] and the newly promoted [[ColonelBadass Lieutenant Colonel]] Sheppard have to go to the hangars and remove the F302 computers by hand. As they finish, however, the virus thinks it's really funny to open the hangar doors into space. The automatic forcefields protect them just long enough to make it into one of the F302s, which have their own oxygen supply. Their continued breathing assured (at least for the moment), Colonel Caldwell reboots the Daedalus a second time.

Which still doesn't work, because there's one last pilotless F302 ''outside'' the ship, continuing to provide a safe haven for the virus. Sheppard takes his plane (with a reluctant [=McKay=] along for the ride), and dogfights the other fighter. He eventually manages to destroy it, the Daedalus gets rebooted a third time, and they all return safely home to Atlantis.

* HaveYouTriedRebooting: see quote. It works...eventually.
* ExplosiveDecompression: averted. The poor guy just sort of falls out through the airlock as the pressure equalizes, without any undue windiness or explosion.

-->'''Hermiod:''' ‘Crap’, indeed

* YouHadUsWorriedThere: Twice. First after the virus vents the amosphere in the fighter bay, then again after the battle in the corona of the sun.
* ZeroesAndOnes: The computer monitor behind Hermiod displays the virus as scrolling columns of zeroes and ones...until they "translate" it into Wraith.

* CallBack: [=McKay=] compares the situation to the [[StargateSG1 SG-1]] episode "Entity."

The solution is to reboot the entire ship, then restore the systems from clean back-ups. Unfortunately, the virus is able to hide out in the computers of the F302s in the hangar bays, and re-establishes itself almost instantly. [[ItGotWorse Worse]], it now has enough control of the Daedalus to direct it to fly into the coronosphere of the local star, which will bake all the people to death while leaving the ship itself largely intact.

---> -- '''Sheppard''' is skeptical of the plan to reboot the ship.

* CutTheJuice: see quote. It works...eventually.