Celebrations are cut short when the Galactica is under attack from a computer virus and Cylon Centurions. The Cylons boarded during the firefight that took place before they jumped to join the rest of the fleet in the last episode. Capt. Lee Adama ( Apollo ) leads the fight against the intruders before the team splits into two. Apollo leads a team of soldiers to track down the Centurions. The other team which includes the President Laura Roslin, Petty Officer Dualla and Billy Keikeya are more concerned with surviving. After a cat-and-mouse adventure, Apollo builds a barricade to ambush the Centurions. However the plan doesn't go to plan as Billy lets off his weapons and alerts the Centurions.
Cpl. Tyrol and Cally rejoin the landing party on Kobol. The man who they had gone to get the medikit for dies from his injuries. Dr. Gaius Baltar continues to dream, first that he's been found by Adama who then kills his and Number Six's baby. The second time is when Six tries to manipulate him through skulls of the dead.