With a Goa'uld mothership en route to attack Earth, Dr. Elizabeth Weir has ordered the Goa'uld dignitaries Camulus, Amaterasu, and Yu detained. Across the galaxy, the Asgard Penegal informs Thor and Teal'c that stray Replicator blocks from the destroyed Replicator vessel have rained down upon the Asgard colony on the planet Orilla. The blocks have infected portions of the cities that contain the technology that enables Asgard preserve their consciousnesses in computer mainframes, giving the Replicators a decided advantage in conquering the remains of the Asgard civilization.

Hoping to stop this threat with the Ancient knowledge in Colonel O'Neill's mind, Thor, and Teal'c rush to Earth. At the S.G.C., Daniel reports that the Goa'uld mothership en route was destroyed by Baal's forces, and that the Goa'uld collective are bowing to his power. Daniel is suddenly whisked away to the Asgard ship, along with O'Neill's frozen form. Thor interfaces O'Neill's mind with the ship, hoping Jack will provide them with the information they require to defeat the Replicators before they heal him by removing the Ancient library downloaded into his brain ("Lost City, Part 1"). Jack appears as a holographic projection, and almost immediately he begins to construct something.

A very much alive Sam Carter awakens to find herself on a farm, and discovers her boyfriend Pete Shanahan feeding livestock. Realizing her memory is missing pieces, he says that they've moved to Montana. A year before she left the S.G.C. because of mental stress, and to be with him. Since then she has been seeing a shrink due to terrible nightmares about the Replicators. Though she is skeptical of this reality, Sam agrees to breakfast.

Yu's First Prime, Oshu, requests an audience with Dr. Weir, and announces that he will die before revealing any information – and that nothing his master says can be trusted. He asks that they be freed to fight against Baal's forces (who may very easily rule the galaxy if he manages to defeat the remaining System Lords), or if they must, die with honor in fighting to destroy him. After discussing the situation with her superiors, Weir agrees to release the System Lords. But to her surprise, Camulus requests asylum. His forces had been among the first to fall; he would have nothing to return to but shame and, ultimately, death.

Soon Yu, Oshu, and Amaterasu depart from Earth, swearing that Camulus will be remembered as a traitor and a coward.

Sam remains skeptical that her and Pete's life in Montana is a reality, until Shanahan reveals himself to be the humanoid Replicator Fifth, who has invaded her mind again. He tries to persuade Carter to get on with her life in his care. Having moved beyond his anger over her betrayal, Fifth professes his love for her. Carter swears that she would never be happy in his fantasy, but Fifth has no other plans for her and warns that if she does not comply, she can live here unhappily for the rest of her life.

As the Asgard stasis unit sustaining O'Neill's life begins to fail, Jack completes the design for a device in conjunction with the ship's computers. Thor wipes the knowledge of the Ancients from his mind, and O'Neill is resuscitated. He is unaware of the purpose of the device he has constructed, but Thor believes it may indeed be a weapon to defeat the Replicators.

The Asgard Penegal informs the team that the Replicators on the surface of Orilla are behaving in a pattern unlike any previously seen, and are likely being controlled by a single humanoid Replicator. He also reports that scans of the surface reveal no sign of Major Carter. Asgard commander Aegir soon reports a loss of all contact with the colony on Orilla – but that he has discovered a single humanoid Replicator floating in space. Thor transports it aboard and SG-1 arm themselves. Thor begins to retrieve communication data referencing any other human-form Replicators, and discovers that Carter is indeed still alive in a Replicator structure near a large vein of neutronium beyond the colony. The Replicators require neutronium to construct their human-form brethren, Thor tells the team – and Orilla is rich in neutronium because it is also important to rebuilding the Asgard civilization.

Almost immediately the transmission is cut as the humanoid Replicator awakens, escaping from the pod and commandeering Teal'c's weapon. On instinct, O'Neill grabs the device he has constructed and fires it at the Replicator, rendering all of its component blocks inert. Having seen the device in action, Thor is now able to create a large-scale weapon from the data stored in the computer to wipe out all of the Replicators on Orilla. He transports SG-1 to the surface in the hopes of freeing Carter.

The team is confronted by hundreds of Replicators. SG-1 fires at will, but are soon intercepted by Fifth, who warns that any more destruction of his brethren will result in Carter's instant death. They have no choice but to comply. Fifth returns to Carter, telling her that the Asgard have developed a weapon against his species. Carter makes one final declaration that if Fifth has a shred of humanity and truly loves her, he will free her.

Thor successfully powers the larger-scale weapon on his ship and discharges it over the Asgard colony, destroying all remaining Replicators – while Fifth's newly constructed Replicator ship flees Orilla into hyperspace. O'Neill, Jackson, and Teal'c find Sam alive nearby.

After the team returns to Earth, Dr. Weir announces her reassignment to head up the research project at the Atlantus outpost in Antarctica. The S.G.C. will now be overseen by a Brigadier General named ... Jack O'Neill. General Hammond will oversee a new secret department that is unofficially being called "Homeworld Security," which includes Stargate Command, Prometheus, and the ongoing 303 construction project. After consulting his teammates, Jack accepts the promotion and the new position. His first order of business: promotion of Major Samantha Carter to the rank of Lieutenant Colonel.

Fifth's escape vessel has managed to reconstitute itself into the previous, more advanced form that escaped the Halla system. Inside, the neutronium they retrieved from Orilla is formed into his new companion: a humanoid Replicator duplicate of Samantha Carter, who he hopes will help him conquer the galaxy.