Drs. Weir and McKay and the newly promoted Lt. Col. Sheppard are en route from Earth to Atlantis on board the Daedalus. Their first visit home has been emotionally draining, and they are looking forward to resuming their lives in the Ancient city.
Soon after they cross into the Pegasus galaxy, however, a scientist is electrocuted in the Daedalus's computer room. McKay first believes that faulty circuitry is to blame, but then a second scientist is killed while investigating the problem. Now convinced that the deaths are no accident, McKay convinces Col. Caldwell, commander of the Daedalus, to drop the ship out of hyperspace until the murderous saboteur can be found.
With the help of the ship's Asgard advisor, Hermiod, McKay quickly discovers that the saboteur isn't a person at all - it's a Wraith computer virus. It seems to possess some form of artificial intelligence, allowing it to predict the actions of its human opponents and rewrite itself in response. Unless those on the Daedalus can stop it, it will fly the ship straight to the Wraith, giving them access to all the advanced human and Asgard technology aboard.
When McKay attempts a full system shutdown, the resilient virus responds by flying the ship straight toward the coronasphere of a nearby star. The route will not destroy the ship, but the intense radiation will kill everyone aboard, freeing the virus to continue its mission without interference. As they zoom toward the star, Sheppard, McKay and the others know they will have to find a solution quickly if they want to see their new home again.