- I'm just saying that if we're taking a page from the John Sheppard book of computer repair, we're really desperate.— Sheppard is skeptical of the plan to reboot the ship.
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 the battle with several Wraith hiveships. 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 F-302s in the hangar bays, and reestablishes itself almost instantly. 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 Lieutenant Colonel Sheppard have to go to the hangars and remove the F-302 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 F-302s, 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 F-302 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.
Tropes
- Absence Makes the Heart Go Yonder: In one flashback it is revealed that Simon has "met someone" while Dr. Weir has been away on Atlantis. This is not terribly surprising given that in her last message (read, only) she encouraged him to move on with his life.
- Anachronic Order: The flashback scenes to earth.
- Call-Back: McKay compares the situation with the Wraith AI to a very similar situation SG-1 experienced 5 years earlier during the events of "Entity".
- Computers Speak Binary: The computer monitor behind Hermiod displays the virus as scrolling columns of zeroes and ones… until they “translate” it into Wraith.
- Character Overlap: General Hank Landry. Since O'Neill has stepped down from command of the SGC at this point in the franchise 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 during Seasons Two and Three.
- Colonel Badass: Sheppard thanks to his promotion to Lt. Colonel.
- Continuity Overlap: 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, Part 2" and the Season Nine premiere "Avalon, Part 1" (as the Daedalus 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.
- Contrived Coincidence: 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 — and by the time it had, the Daedalus had left Pegasus and arrived in the Milky Way. So, it's remained dormant until the ship was once again back in proximity to Wraith territory.
- Early-Bird Cameo: Since the flashbacks take place prior to "Avalon, Part 1", this episode is technically the first chronological appearance of Hanky Landry in Stargate.
- "Eureka!" Moment: Hermiod's observation that the computer virus is unlike any human-created program he's seen before. This comment is what inspires Rodney to run a Translation Program to confirm or disprove his fears that it's actually a Wraith-created virus.
- Explosive Decompression: Averted. The poor guy just sort of falls out through the airlock as the pressure equalizes, without any undue windiness or explosion.
- Foreign-Language Tirade: An irritated Hermiod again cusses out the Tau'ri in Asgardian, cementing this as a minor running gag.
- Have You Tried Rebooting?: see quote. It works… eventually.
- Hero Antagonist: 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).
- Military Maverick: Sheppard's pre-Atlantis history of doing this nearly bites him in the ass again. Because of the events of "Hot Zone" (and Sheppard disobeying a direct order from Weir), Landry, Caldwell, and the SGC have reservations about him remaining part of the Expedition and answering to a new military commander. From their perspective, if Sheppard was willing to openly defy the Expedition's civilian leader, they can't trust him not to do the same for a new military commander.
- Motive Misidentification: If the virus was uploaded to the Daedalus by the Wraith Cruiser that drew parallel during the second battle in the preceding episode, then Sheppard's assessment was wrong. It wasn't trying to board them, but was instead trying to get within transmitting range.
- Oh, Crap!: On learning the virus is Wraith in origin.McKay: Crap.Hermiod: What did you do?McKay: I just ran (the virus) through a translation program. It’s Wraith.Hermiod: “Crap”, indeed
- Passed-Over Promotion: Caldwell was the favored candidate to replace the late Colonel Sumner as the Expedition's military commander (and also presumably with Colonel Everett having been WIA during the Siege). 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 on the flight back to Pegasus.
- Rank Up: Thanks to Weir's lobbying, Sheppard is promoted from Major to Lt. Colonel to allow them to remain in command of the Expedition's military contingent.
- The Reveal: The Wraith covertly uploaded a virus into the Daedalus 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).
- Screw the Rules, I Have Connections!: When Landry and Caldwell try to replace Sheppard as Atlantis' military commander, Weir reminds them that she was appointed to lead Atlantis by the President and she's still in favor. So, she has no hesitation playing that card to keep Sheppard on the Expedition (and does).
- Smart People Play Chess: Invoked by Sheppard when McKay compares the current situation to a game of chess. Rodney says that he would play chess more often, but he can't find challenging opponents at Atlantis.
- Teeth Clenched Team Work: Rodney and Hermiod have a...strained working relationship.
- Thrown Out the Airlock: Lindstrom's fate.
- You Had Us Worried There: Twice. First after the virus vents the atmosphere in the fighter bay, then again after the battle in the corona of the sun.
