Scouring the Atlantian database Dr. Rodney McKay (David Hewlett) discovers a reference to an abandoned Ancient testing site. Investigating the site, the team discovers a vast metropolis supporting millions of Ancients. Eager to create an alliance with such an advanced society, Weir (Torri Higginson) is shocked when their leader Oberoth (David Ogden Stiers) refuses the offer. Seeing no way to appeal to their humanity to help save the Pegasus galaxy from the Wraith, Weir and the team head back to Atlantis. However before they are able to leave, the team is ambushed and taken prisoner by Oberoth and his guards. The team is then subjected to a mind probe by what they now discover are actually replicators in the form of Ancients. Having created the replicators as a weapon against the Wraith, the Ancients feared they were losing control of their creation. But the Ancients' attempts to destroy the replicators failed. Now, the surviving replicators are divided - some wish to mimic their creators and seek ascension. Others, including Oberoth, want nothing more than the destruction of Atlantis as revenge for the Ancients' betrayal. Now the team must find a way to free themselves and stop the replicators from reaching Atlantis.