Sheppard is returning from a solo supply mission, traveling by Puddle Jumper, when someone attacks him. The attackers' weapon disables his systems, causing him to lose contact with Atlantis, and the intruders' ship takes him on-board then jumps into hyperspace.
The human crew brings Sheppard on-board and take a blood sample, then interrogate him for information, beating him when he refuses to answer. Meanwhile, McKay tries to track down the enemy ship without much luck.
The ship's commander, Larrin, comes in and Sheppard tries to negotiate. Larrin agrees to talk and reveal that her race are nomads who live on their spaceships. She's interested in the Ancient genes that he has and isn't convinced when he plays dumb. She then puts him in the hanger and opens the hangar doors, with only a force field between him and deep space. She then shows him an Lantean battleship and insists that he help make it functional.
Bringing Sheppard back on, they reveal why the ship has been drifting in orbit around a dwarf star. Sheppard activates the ship, using the inertial dampers to knock the crew out and then take the ship into hyperspace.
Rodney, Ronon, Teyla, and Lorne search for Sheppard without success, and McKay warns there's nothing they can do.
Larrin tries to convince Sheppard to surrender, shutting down the fields protecting the bridge from radiation. Sheppard has no choice but to surrender and Larrin puts him in the brig. Sheppard shut down all the systems but her science officer, Nevik, can't obtain enough recorded information to pilot the ship on their own.
Back on Atlantis, McKay picks up a signal from Sheppard.
Larrin walks into Sheppard's cell and slugs him, telling him that they know about the signal and now a Wraith ship is approaching them. It opens fire and Larrin has no choice but to let Sheppard take control. They lose all power to the shields and the Wraith score a direct hit. Sheppard manages to enable the attack drones and destroys the Wraith ship. Larrin's people were killed in the blast and she's the only one left. She arrives on the bridge only to find Sheppard gone. He goes to the auxiliary control room and locks her in, then shuts off the transmitter. Larrin tries to get Sheppard to release her but he isn't buying it.
The Atlantis team travel to Sheppard's reported position and they detect the ship several light years away. Lorne orders the other Puddle Jumpers to rendezvous at their location.
Larrin works to override the system and Sheppard cuts her off from the systems. She tries to persuade him that her people need a new ship but he refuses to let her go so she blasts her way through the door. He confines her with corridor force fields and confirms that her people are dead. He picks up another life form in front of her and she opens the door… only to find a Wraith. It quickly disarms her but she stabs it through the hand. She's no match for it in hand-to-hand but Sheppard guns it down and confirms that there are three more on the ship. When it comes back to life, Sheppard has to finish it off for good but they're low on weapons.
Using a portable lifesigns detector, Sheppard tracks the other Wraiths and takes refuge in a storage chamber to conceal themselves.
The Puddle Jumpers close on the battle cruiser while McKay wonders what is going on. Sheppard and Larrin emerge and Sheppard reveals that he didn't have time to shut down the controls so the Wraith can take control. Larrin suggests that they lure the Wraith away from the center of the ship and use the drones against them. Sheppard goes to the control room while Larrin lures two of the remaining Wraith away into another section. Sheppard then blasts the section open with a drone, sending them into space. The remaining Wraith attacks and starts draining her life force, and Sheppard goes to investigate. The Wraith tries to interrogate her but Sheppard puts a gun to its head to force it to restore Larrin's life force then leave the ship and head for a nearby planet. The Wraith has no choice but to agree but when Larrin revives, she kisses Sheppard in appreciation… then stuns him unconscious.
Larrin goes to the control room and reveals to Sheppard that her ships have arrived first. They send over a security team to capture Sheppard. McKay's team arrives under cloak and detects all of the ships, but don't know which ship Sheppard is aboard. McKay tries to figure out a way to disable their ships.
Larrin confronts Sheppard and insists on keeping him onboard to help her regain control of the systems. He tries to persuade her that finding a new ship is a stopgap measure at best and suggests an alliance against the Wraith. McKay and the others prepare to open fire when the ships depart into hyperspace. They get a contact from Sheppard in his Jumper: Larrin released him before departing.
Back on Atlantis, Sheppard enjoys a fresh meal while McKay complains that he never gets taken prisoner by sexy aliens. Sheppard warns that Larrin is still out there, and considers the fact they'll meet again.