With many of the original party returned to their own time, Varian, Scott and Fred find themselves caught up in the machinations of a being called The Source, which has enslaved the inhabitants of the city of Atlantium, built by the survivors of the original Atlantis. The Source plans to use Scott's life force to regenerate itself. The trio are aided by Liana, who reveals that she is half alien.

Scott is made to join a colony inhabited solely by children led by the bullying teenager Alpha. Their forebears lived in a society decimated by war and the group inherited a deadly weapon used to keep any elders from over taking their leader.