Scouring the Atlantian database Dr. Rodney McKay 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 is shocked when their leader Oberoth refuses the offer.

Summoned to a planet by a communication code they had previously given their Genii allies, the team is ambushed by Kolya, who has now created his own faction of Genii after being forced from the inner circle of the Genii leadership. While the rest of the team manages to escape, Sheppard is taken prisoner.