As the premiere for the second season unfolds, Adama lay dying leaving Tigh in command. Lee and Roslin have been sent to the brig. An emergency jump goes wrong leaving the Galactica alone in space without the fleet.
Gallactica meets Pegasus, and Adama's command is threatened when the captain of Pegasus outranks him. A joyous celebration turns sour at some of the secrets emerging out of the differences of the two crews, and Baltar meets a familiar Cylon prisoner aboard Pegasus.
Galactica and Pegasus are preparing for the assault on the Cylon Resurrection ship. While Starbuck discusses Adama's plan to kill Cain with Apollo, Colonel Fisk stops Pegasus' crew members beating up Helo and Tyrol. He dispatches his marines on Galactica to execute Cain's plan to kill Adama. Apollo seems to dislike his father's plan and hears him out before he sets off in the blackbird to destroy the FTL-drive of the Resurrection ship. It goes wrong for him. Meanwhile Dr. Baltar is trying to take care of the Number Six on Pegasus. He seems to have feelings for her, ...
Apollo investigates the murder of one of the crew and falls for a young prostitute, whom he vows to save from the rogue ship dealing with the Black Market. As well as confronting the bad guys, Apollo has to confront some past mistakes.
The Cylon baby is finally born, leading to some political decisions being made. Meanwhile, the Cylons on Caprica contemplate life and humans when they meet up with a certain human from a previous episode. This story explores the Cylon world.