With Adama out of action, Colonel Tigh takes his position as commander of the Galactica. Boomer is in jail, and the cat's out of the bag - she's a Cylon.

Tigh has to work with Lee to defeat a Cylon boarding party that threatens to take over Galactica and destroy the fleet.

A reporter is sent to Galactica to chronicle the harsh realities of life during wartime.

Sharon helps the Resistance on New Caprica as Adama leads Galactica on a dangerous rescue operation. Tyrol races to save Cally from the execution squad. Meanwhile Anders uncovers treachery among the humans. Number Three meets the Oracle Selloi after having strange dreams about the temple.

Tigh must decide the fate of his wife Ellen after the assistance she rendered to the Cylons. Lee struggles with his assignment to protect the civilian fleet on its journey toward Earth while Adama returns to New Caprica with just the Galactica. The Resistance coordinates an attack on the Cylons just as Galactica arrives. As the Cylons begin to lose control, Number Three vows to put a final end to the New Caprican experiment.

When Baltar's representatives face assassination attempts, Adama asks Lee to protect Baltar's lawyer. After taking on the assignment, Lee seeks to play an active role in Baltar's defense.

Loyalties are made clear when Gaeta orchestrates a coup d'état of the Adama regime. Both prisoners and lives are taken as many of the fed up people work to take over Galactica.

President Roslin faces off against Tom Zarek and Lt. Gaeta as they try to take control of the Colonial fleet. Both the alliance with the rebel Cylons and Adama's life are at stake.