While doing standard recon on a planet thought to have been destroyed by the Wraith long ago, the team finds an Ancient structure standing intact amidst the ruins. After some investigating, they discover that the monolith served as a military research facility where the Ancients worked to develop an advanced method of harnessing energy. When the Wraith attacked before the project could be completed, the underdeveloped technology malfunctioned and destroyed the civilization. McKay theorizes that if the powerful technology is fully developed, it could serve as a potent source of energy for Atlantis. Hope turns to fear, however, when McKay's first attempt at reviving the energy source results in the death of one of the Atlantis scientists. Despite the team's apprehension, a determined McKay insists on moving forward with finishing the project. But can McKay unravel the intricacies of the Ancients' technology without putting himself and Sheppard in mortal danger?

Having been savagely bitten by the Wraith girl Ellia, Sheppard hurries back to Atlantis for medical treatment. Both he and Dr. Beckett are shocked, however, when they realize that the wound has vanished. Sheppard's arm is completely free of any trace of the bite.