Recap: Stargate Atlantis S02 E02 "The Intruder"
I'm just saying that if we're taking a page from the John Sheppard book of computer repair, we're really desperate.
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 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. 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 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.