When a scientist is killed in the Daedalus' computer room, McKay first believes the poor circuitry is at fault. However, when another scientist is killed while investigating the death, McKay begins to suspect that someone – or something – is deliberately planning these breakdowns. Soon after, McKay is alerted to a virus on one of the ship's computers. When he runs its code through a translator, he is shocked to discover that it is written in Wraith. Even worse, he learns that the virus has the ability to re-write itself, making it seemingly impossible to conquer. Realizing that the program's capability to mutate has virtually given it a mind of its own, McKay worries that the Wraith may use the virus to take control of the ship – with potentially deadly results. As feared, the virus' artificial intelligence soon takes control of the Daedalus' auxiliary ships, and the crew becomes increasingly powerless to defend themselves. Fearing that the Wraith will use the Daedalus' advanced features to attack Atlantis, McKay and Sheppard race against the clock to counteract the virus before the Wraith turn the Daedalus' advanced technology against the city.
Spoilers ahead. Coverage follows the scope labeled below.
Complete story — includes the ending
Strange malfunctions begin to occur when newly promoted Lt. Col. Sheppard along with other members of the expedition return from a trip to Earth aboard the Daedalus. When things go too far, they discover that the ship has been infected by a Wraith virus, and now it has the instinct to stay alive, even if it has to kill in order to survive. Meanwhile, periodic flashbacks reveal the events of their visit to Earth including a meeting with Ford's cousin.