Atlantis remains stranded and out of power, in the middle of space. Col. Ellis of the Apollo has reported the city's disappearance, and Col. Samantha Carter and Dr. Bill Lee of Stargate Command travel to the Pegasus galaxy to initiate a search. Carter has a plan to find Atlantis, but it will take time - lots of time. They must hope that they're not too late.
The denizens of Atlantis aren't waiting around for rescue. Rodney McKay modifies a Jumper to fly through hyperspace so a team can travel to the Replicator homeworld and steal a Z.P.M. to power the city. Elizabeth Weir, now part-Replicator herself, agrees to go along because she can link to the Replicators' mind-network and guide her people where they need to go. She is uneasy about her strange new abilities, but determined to help.
Sheppard, Weir, McKay and Ronon fly to the Replicator homeworld, where McKay activates the link between Weir and the Replicators. With new knowledge flooding her mind, Weir guides Sheppard and Ronon as they sneak into the city and steal a Z.P.M. The mission seems accomplished.
McKay, however, makes a crucial discovery by probing the Replicator network through Weir's link. Buried in the sentient machines' base code is a dormant command to attack the Wraith. If the team could activate that command, Atlantis's two greatest enemies would go to war and, just maybe, wipe each other out. It's a riskier mission than stealing the Z.P.M., but it's too great an opportunity to miss.
Sheppard and Ronon trek deeper into the city to the Replicators' central data core. Unfortunately, as Sheppard struggles to activate the command, the Replicators discover them and soon adapt to their anti-Replicator shields and weapons.
With Sheppard and Ronon about to be captured or killed, Weir takes action. She confronts the Replicator leader, Oberoth, outside the core room. Engaging him in a Replicator-style psychic battle, she tricks him into believing that he has defeated her even as she actually freezes all the Replicators long enough for Sheppard to activate the command. Then her control weakens and Oberoth reasserts his power. As the Replicators capture Weir and swarm after Sheppard and Ronon, she orders the two men to leave without her. They barely escape back to the Jumper.
Deeply saddened by Weir's sacrifice, Sheppard flies his team into orbit. Replicator ships are pursuing them, and the Jumper has no power left after the hyperspace flight that brought it here. Unless McKay - or Samantha Carter - can work a miracle, they will die despite Weir's heroism.