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.

A Cylon virus is interfering with Galactica's power supply, while Cylon centurions are heading for crucial systems. Somehow they must be stopped.

Tigh has problems with the responsibility of being a leader, president Roslin loses control without chamalla. The Kobol team discovers a Cylon battery.

Tigh's decision to impose martial law is protested in the fleet as well as on Galactica. On Caprica, Helo and Starbuck meet other humans.

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 Commander Adama tries to join Roslin's team on Kobol, Dr. Baltar's Number Six tells him he's crazy.

Journalist D'Anna Biers is making an item on the Gideon incident, when she's asked by Adama and Roslin to film daily life on Galactica.

While Tyrol decides to start building a new fighter, the Cylon virus is rearing its ugly head again. Boomer says 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.

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, much to the dismay of the Number Six in his head.

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.

A terrorist attacks and holds several key people hostage and threatens to murder them unless she is given the Cylon prisoner.

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.