Col. Sheppard's team is urgently summoned to M1K-177, where Maj. Lorne's team has been attacked. When Sheppard and his unit arrive, however, all they find is a burned building containing charred bodies: presumably, Lorne and his men.
After returning to Atlantis, Sheppard and Weir are startled when Ladon Radim, a member of the Genii strike force that previously tried to attack the city, contacts them through the stargate. He claims that he wants to trade a ZPM in exchange for weapons to stage a military coup against Cowen, the ambitious Genii leader.
Weir, uncertain if Ladon's story is true, orders him secretly followed and dispatches Sheppard and McKay to the Genii homeworld. There, they meet with an unexpectedly friendly Cowen, who dismisses Ladon as an ineffective troublemaker, nothing more. Not sure who to trust, but having learned that Ladon has only about 20 followers at his small encampment, Sheppard and Weir decide simply to raid the place and steal the ZPM. First, they lure about half of Ladon's followers to Atlantis, then Sheppard launches his attack on the base.
Dr. Beckett, meanwhile, discovers a critical clue about Maj. Lorne's team: while the bodies found were wearing Lorne's team's dogtags, their DNA doesn't match. Lorne and his men are still missing. Teyla and Ronon return to M1K-177, but the villagers there seem frightened and unwilling to answer questions. One, however, manages to slip Teyla a satchel containing Genii "wanted" posters of various Atlantis team members, including Lorne, Sheppard and McKay. Weir realizes that all of the people pictured possess the ATA gene - and many of them are on the raid with Sheppard.
Sure enough, Sheppard's men breach Ladon's headquarters only to be gassed into unconsciousness. It's all been a trap; Ladon's been working for Cowen all along. Cowen radios Weir and demands she surrender all ten of Atlantis's Jumper ships - or he'll start killing the hostages.
Sheppard points out that Cowen and his men can't fly the Ancient ships without the ATA gene, but Ladon proudly reveals that he has already captured Lorne and his men. With genetic samples from them, he hopes to artificially reproduce the gene.
Back at Atlantis, Weir tries to trade her Genii captives for Sheppard and the others, but Cowen is adamant. Because Weir refuses to give up the Jumpers, he orders the first hostage executed: Sheppard.