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Chaos is rampant as paramedics try to save Commander Adama's life, and the Galactica is separated from the fleet. Suspicion is cast on even the closest of allies.
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As Commander Adama lies near death, Colonel Tigh must face the civilian government -- who fear the commander was instigating a coup by arresting President Roslin. The survivors on Kobol face a crisis when Crashdown orders an attack on the Cylons.
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Apollo orchestrates an escape for Roslin and her supporters, while Tigh's suspicions about Cylon operatives fall on Chief Tyrol. Kara and Helo fall in with a group of humans who have survived on Caprica and started a resistance movement.
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Kara is shot and wakes up in a remote hospital facility on Caprica, and learns that her friendly doctor has his own plans for her future. Commander Adama attempts to recover from his injuries.
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Lee joins President Roslin and Tom Zarek in a separatist fleet determined to explore Kobol, forcing Commander Adama to find a new flight leader for the Galactica.
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Adama joins President Roslin and her team on the surface of Kobol, intent on reuniting the fleet. Six tells Baltar that he is going insane.
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A reporter is given full access to Galactica to document military life after criticism of the military reaches a fever pitch.
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The crew is stunned to learn that the Battlestar Pegasus also survived the attack on the Colonies, but tensions run high when the Pegasus's Admiral Cain assumes command of the fleet. Baltar is assigned to examine the Pegasus's own Cylon prisoner, a battered woman who looks like Number Six.
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President Roslin lies on her deathbed, recalling her life on Caprica in the final hours before the attack. A terrorist group surfaces in the fleet demanding peace with the Cylons, and Baltar makes a discovery about the Cylon Sharon's unborn child.
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Lee becomes entangled with a mafia-like group of criminals when he invesitages the murder of a Colonial officer -- and is reunited with a former lover.
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The Colonial fleet is plagued by a mad Cylon raider, a living ship that continues to assault the fleet with hit-and-run attacks.
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A woman who lost her husband to the Cylons takes the Cloud Nine lounge hostage, demanding that Adama hand over the Cylon Sharon so that she can exact revenge.
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The reincarnated Number Six and Sharon struggle with their past lives on Caprica, where they are heroes of the Cylons. On Galactica, another Sharon gives birth to her hybrid child.
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