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.
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.
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.
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.
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.
The Galactica is struck with a Cylon computer virus that threatens to kill the crew, forcing Adama to go to their Cylon prisoner. Chief Tyrol throws himself into the impossible task of building a Viper from scratch.
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.
Adama and Admiral Cain must put aside their differences when they receive new intelligence about a Cylon "Resurrection ship." But a new revelation about Cain's past actions could unravel their alliance entirely.
As the Battlestars Galactica and Pegasus launch an attack on the ship that allows Cylons to be downloaded and reborn in a new body, Adama and Cain also plot one another's assassinations.
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.
Lee becomes entangled with a mafia-like group of criminals when he investigates the murder of a Colonial officer -- and is reunited with a former lover.
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.
Tension runs high between Lee and Kara and the new commander of the Pegasus when a Raptor scouting party goes missing. The arrival of a pregnant girl seeking refuge on Galactica erupts into political chaos for President Roslin.
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.
As Roslin and Baltar jockey for position leading up to the presidential election, Kara leads a dangerous mission back to Caprica to rescue members of the resistance.
With Baltar advocating permanent settlement on a hidden planet, President Roslin is faced with a crucial ethical dilemma on election day. The crew is stunned when the Cylons send representatives with an overture of peace.
