Sheppard's team is lured into a brutal ambush by a message that appears to come from Ladon Radim, the new Genii leader. McKay, Teyla and Ronon escape their mysterious assailants, but Sheppard is captured and taken to an unknown planet. When Weir demands that Ladon comes to Atlantis to explain, he willingly agrees, swearing that he's innocent and insisting that the identification codes used in the message were stolen from him.
Sheppard finds himself the prisoner of his old nemesis Acastus Kolya, a renegade Genii warrior. Kolya believes that Ladon stole his rightful place as the leader of their people - and he plans to rectify that betrayal. After his spies inform him that Ladon is in Atlantis - just the move he hoped Ladon would make - he contacts the city with a video signal. As Weir and the team watch with horror, Kolya allows a captive Wraith to feed on Sheppard. He warns Weir that he will repeat this monstrous act every three hours until Weir turns over Ladon - or until Sheppard is dead.
Kolya expects that Weir will be too softhearted to resist, but she knows that submitting to his demand is as bad as negotiating with any other terrorist. If they want Sheppard back, they must rescue him themselves. Accordingly, McKay enlists Ladon's help to track down Kolya's stronghold, but after a dramatic raid on a suspicious Genii outpost, they come up empty. Ladon swears he's doing his best, but Weir and her people have had too many dealings with the devious Genii to trust him.
Sheppard, meanwhile, has made an unsettling discovery: the prisoner in the cell next to his is the captive Wraith. Kolya is torturing them both: Sheppard during the painful feedings, and the starved Wraith during the hunger-filled intervals between them. Both initially refuse to feel sympathy for the other. As two more torturous feedings go by, however, they accept that they share one common goal: to escape. Thus, working together, they break out and flee into the woods outdoors.
But after the suffering they've endured, they don't have much strength left. Exhausted, they must hope that Sheppard's friends rescue them soon. Until then, their survival depends on the uneasy truce they've established. Similarly, the success of the rescue mission depends on Weir's uneasy alliance with Ladon. If either the Wraith or the Genii breaks his word, Sheppard will never make it home.