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.
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.