Atlantis discovers one of the Ancients’ abandoned research outposts, that turns out not to be abandoned.
However, they find they have found a Replicator community living in an even greater “Atlantis like" city, part of which also has the capable of space flight. The learn the Replicators have always wanted to emulate the Ancients, and have also wanted to exceed them. However, they want, but can’t duplicate the Ancients’ final step of ascending.

Now the Atlantis team must escape these Replicators, but not before they also extract the knowledge they have to defeat the Wraith.