Col. Sheppard and Dr. McKay are enjoying some recreational time on the pier level of the city when Atlantis is plunged into darkness, with only the top tier of the central tower unaffected. Struggling to make their way up to the Gate Room on foot, more than 70 levels above, McKay speculates that someone has taken control of Atlantis by hacking into the city's mainframe. As they close in on the location, McKay picks up extreme energy readings. An unusual force field has been established to prevent them from gaining access to both the Gate Room and Control Room.
Meanwhile, as Teyla checks on her son, Torren, two dark figures infiltrate her quarters and fire, rendering her unconscious. When she comes to, she finds herself in Woolsey's office with the baby sleeping nearby. Distraught, she moves to reclaim him, then realizes she is not alone. Her ultimate nemesis, Michael, stands before her, and he is bent on revenge.