Ronon and Teyla arrive at a village investigating reports of Wraith-killers who may be Ronon's people, the Satedans. Teyla quickly finds them in a tavern and gets into a fight, but Ronon arrives and recognizes them all.
Back on Atlantis, Rodney believes he'll be chosen as the new leader of Atlantis. Sheppard is checking in with Sam Carter on Earth and Rodney stops in to accept their congratulations, only to find that the IOA has chosen Sam to head Atlantis.
Ronon sits down with his comrades, Tyre, Ara and Rakai, and they explain how they escaped from the Wraith. They've heard that Ronon was chosen as a Runner and are duly impressed.
Sam bids Teal'c goodbye then heads for Atlantis where the team prepares to greet her and Rodney tries and comes up with a suitable welcoming gift.
While Ronon gets a new tattoo, the Satedans reveal that they've lost two of their teammates. Rodney shows up with flowers for Sam, only to find that Sheppard has upstaged him. After blathering about their relationship or lack thereof, Ronon arrives and asks to bring the Satedans to Atlantis. Sam refuses based on IOA orders and a disappointed Ronon returns back to the Satedans where Tyre notes that the Atlanteans may be his allies, but the Satedans are his friends and they want Ronon to join them.
Sheppard talks to Sam who notes that Sheppard was also considered, but he claims he wasn't interested due to the politics, and he plans to find Weir. Sam refuses to authorize a mission without a solid chance of success and Sheppard accepts it.
Ronon spars with Teyla but she easily beats him and he finally admits that he's distracted. He admits he plans to leave Atlantis and Teyla says she can understand leaving her people to help Atlantis. Sheppard then meets with Ronon later, and Ronon gets him to hear a plan the Satedans have come up with to attack a Wraith lab. The Satedans need Sheppard's team to provide an escape. Sheppard suggests they wait until the Wraith/Replicator battle settles down but Ronon reveals the Wraith are working on a way to override the Replicator activation code. Sheppard agrees and afterward Ronon tells him that this will be his last mission for Atlantis.
Back on Atlantis, Sam goes to see Ronon but he says he still plans to help Atlantis. She warns it may not be easy to coordinate between the two groups, and he wonders if she'll try to stop him because he poses a security risk.
The two teams arrive by Puddle Jumper through the gate and land near the Wraith lab. Tensions are high and Sheppard finally agrees to follow the Satedans until they're inside. They take out the Wraith guards and make their way to the teleporter and beam inside. The two teams split up and Sheppard's team finds test subjects but can't do anything for them. Sheppard wonders if it's a trap as they stumble into a Wraith patrol. Teyla is stunned and Rodney tries to get them through a door while Sheppard holds off the Wraith. Ronon abandons the Satedans to help and takes out the Satedans, while Rodney gets through the door. Sheppard takes a stun blast and the Wraith haul him and Teyla away. They look for Rodney, unaware that he's hidden among the test subjects. He emerges only for the Satedans to stun him and turn him over to the Wraith.
Ronon gets back to Atlantis and demands to talk to Sam, while Sheppard's team wakes up in a cell. Rodney explains who stunned him and is then taken away by the Wraith. Ronon gets his wounds taken care of and explains what happened, then says that the Wraith will be expecting them. Sam readies two Jumpers to go back and prepares to lead the mission. She tells Ronon that she'll accept whatever decision he makes.
The Wraith want Rodney to undo the programming changes so they can upload the deactivation code again, and have a Replicator soldier imprisoned that he can work on. One Jumper lures the Wraith away while Sam's Jumper comes in from another angle. They get inside the base and rescue Sheppard and Teyla, while Ronon splits up to check out more ground. He runs into the Satedans and the Wraith, and the Satedans reveal their true colors.
Sheppard and the others find Rodney then release the Replicator. It ignores them and goes after the Wraith, while Ronon demands answers. The Satedans admit they're now Wraith worshippers, given the gift of ever-lasting life after torturing them with energy drains. Ronon refuses to join them and they engage in traditional Satedan hand-to-hand combat, three-on-one. He takes out Ara and Rakai temporarily and fights with Tyre. Rakai draws a knife, breaking the code of honor, and when Ara tries to stop him he kills her. Tyre gets the drop on Ronon, but runs away. Ronon joins the others, acknowledging they're his friends, and they head back to Atlantis.
Later on Atlantis, Teyla meets with Ronon and welcomes him back to Atlantis, and he admits it's good to be back. After she leaves, he considers a painting of Satedan glory and honor…