Condemned: The team visits a technologically advanced planet inhabited by a civilisation mysteriously unharmed by the Wraith.
The team tells Weir of their discovery. However, she begins to suspect that the idyllic environment may be the result of a sinister pact between the planet's leader and the Wraith.

TrinityThe Atlantis team may have found a new source of energy for their city based on unperfected Ancient technology. Hope turns to fear, however, when McKay's first attempt results in a death. Can McKay unravel the intricacies of the Ancients' technology without putting himself and Sheppard in mortal danger?

INstinct: The team encounters a scientist, Zaddik, who has been living with a Wraith child, Ellia. Dr. Beckett meets with Zaddik, hoping he can begin a controlled experiment on Ellia with a retrovirus he has been developing. However, the underdeveloped formula has the opposite of the desired effect.

Conversion: Following his encounter with a mutated Wraith child, Sheppard begins exhibiting symptoms similar to the ones that plagued Ford following his own Wraith attack. Dr. Beckett realises that a small amount of the retrovirus, is now in Sheppard's bloodstream. The team races against the clock to save his life.