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.
Tigh has problems with the responsibility of being a leader, president Roslin loses control without chamalla. The Kobol team discovers a Cylon battery.
Starbuck finds herself wounded in a hospital on Caprica where she is suspicious about her doctor. President Roslin makes an appeal to the fleet to follow her to Kobol.
Starbuck, Helo and Boomer bring back the Arrow of Apollo, but Boomer doesn't seem welcome. Commander Adama wants to keep the fleet divided and appoints a new CAG.
While Tyrol decides to start building a new fighter, the Cylon virus is rearing its ugly head again. Boomer tells it means a large Cylon attack is imminent.
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.
Adama and Cain find common ground when Starbuck returns with footage of the Cylon ship. Roslin negotiates a temporary truce, while Starbuck plans an attack.
Starbuck and Fisk are preparing for the murder jobs, while the attack on the Resurrection ship is planned. It goes wrong for Apollo. Dr. Baltar has feelings for Pegasus' Number Six.
President Roslin, who is about to die, believes Sharon's baby is dangerous and orders it must die. Meanwhile, a terrorist group inside the fleet starts to ask for a peace negotiation with the cylons.
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.
This is an episode about loss. Kat and Starbuck confront each other about their piloting skills and each vow to kill Scar (a Cylon spaceship) before the other.
Two of Pegasus' raptors go missing after a suspicious distress call. President Roslin must make a decision on abortion that could hurt her political career.
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.
While Dr. Baltar is behind in the polls for the election and tries desperately to turn things around, Starbuck is planning a mission to rescue Anders from Caprica.
The group on Caprica is under fire by the Cylons, but suddenly they stop. With only one ship's votes to be counted, Roslin is way behind in the elections.
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