Intruder

S2 E2: When a scientist is killed in the Daedalus' computer room McKay (David Hewlett) 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 (Joe Flanigan) race against the clock to counteract the virus before the Wraith turn the Daedalus’ advanced technology against the city.