The Atlantis team goes against orders to try and save Atlantis from Replicator control — and to rescue General O’Neill and Richard Woolsey, who are trapped in the occupied city.

Elizabeth Weir wakes up in a mental institution, where she is told that the expedition to Atlantis and the Stargate are figments of her imagination.

Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, but discover that they may not have left Atlantis in peace.