Major Lorne is under attack on M1K-177 and Sheppard's team is summoned to help by Dr. Lindsey. They find a building that has been exposed to heavy fire, and find the charred remains of what appear to be Lorne and his team going by the dog tags. Back at Atlantis, Sheppard is briefing Weir when they receive an unauthorized gate transmission and get a message from Ladon Radim, a Genii who is aware Atlantis is still intact. They respond and Ladon offers a ZPM.
McKay is in favor of getting the ZPM and Weir considers the deal – finally she agrees over Sheppard's objections, while Ronon and Teyla continue to pursue the investigation into Lorne's death. They dial up the coordinates Ladon provided while Ronon and Teyla talk to Lindsey who claims the villagers are friendly. Then she says she heard Wraith fire and went for help. Ladon is brought to Atlantis but reveals he's hidden the ZPM and will only talk to Weir. Beckett determines the corpses are not Lorne and his team and Ronon and Teyla go to investigate.
Weir meets with Ladon who asks for machine guns and warns the Genii have operational nuclear weapons. He's planning a coup, and wants Weir to help him. He believes Cowen is power-mad and will give them the ZPM in return for their help. Ronon and Teyla pursue the investigation at the village and a barkeep warns someone is watching and will kill them all if he talks, and "they" can't be fought.
Weir and Sheppard are both suspicious and Sheppard sends his special ops men to follow Ladon. A woman makes contact with Teyla and Ronon and slips them a satchel. McKay and Sheppard visit Cowen who dismisses Ladon as a troublemaker whom the Genii have been devoting all their efforts to recover. Cowen appreciates them giving him the info on Ladon and it appears both sides are reconciled despite their past differences.
Sheppard's men have found the warehouse where Ladon is operating out of and Sheppard suggests they steal the ZPM while having some of Ladon's people come through to get supplies, thus splitting their forces. Meanwhile Ronon and Teyla examine the satchel and find that it has wanted posters for the Atlantis people…and many of them are on the raid with Sheppard and have the Ancients gene.
Ladon's sister Dahlia and her people come through the Gate to Atlantis and are taken prisoner. Sheppard launches his raid but realizes it's a trap – Ladon is waiting for them and gives them the ZPM… but it's unpowered. Ladon releases a gas that knocks Sheppard and McKay out. On Atlantis, Beckett determines the unidentified corpses died of radiation poison – the Genii. Weir figures out what's going on, while Ladon wakes up Sheppard and reveals he's working with Cowen. The Gate activates and Cowen contacts Weir – he demands all ten of the Jumpers and will kill one of the team every 15 minutes until his demands are met, starting with Sheppard. Weir attempts to offer Ladon's people back but they're terminal and Cowen knows it.
Sheppard points out the Genii can't fly the Jumpers without the Ancients gene, but Ladon notes that they have the gene and can artificially reproduce it… thanks to samples they've taken from Lorne's team, who are captives. Beckett is working to cure their captive Genii and believes he can help most of them. Weir tells Cowen of this but he isn't interested. Ladon goes to kill Sheppard while Beckett suggests they offer a Jumper and Ronon argues against it. Ladon asks Sheppard if Beckett is telling the truth and decides to let him and the other prisoners go so his sister can be cured. He has a nuclear device beneath the building and is conducting a double-bluff – he plans to kill Cowen and start the coup and needed the Atlantis team to lure Cowen out of hiding.
Cowen gets word that the prisoners are free while McKay and the rest of the team come through the Gate. Sheppard and Ladon come through and Ladon triggers the nuclear explosion, killing Cowen. Ladon is reunited with his sister after Beckett cures her, and Weir offers medical treatment to the rest of the Genii. Sheppard and Weir are happy that they may have made a permanent alliance with the Genii.