Battlestar Galactica was not the only Battlestar to have survived the cylon attack, The Battlestar Pegasus also survived.

The Battlestars Galactica and Pegasus face a new Cylon target, a "Resurrection" ship, while a power struggle threatens to result in all-out war among the human fleet.

Lingering feelings of rage lead Saul Tigh and Kara Thrace to cause problems aboard Galactica between the survivors from New Caprica and those who stayed with the fleet during the Occupation. Baltar assists the Cylons in an attempt to stay alive and uncovers details about Cylon civilization. A Cylon baseship falls victim to a mysterious disease.

Apollo formulates a plan that threatens the very existence of the Cylon culture. Adama and Roslin must decide whether to follow through on the plan to use a biological weapon against the Cylons. D'Anna Biers (Number Three) believes Baltar knows who created the virus that infected and disabled the Cylon baseship. She is willing to take extreme measures to learn the truth.

The Colonial fleet faces starvation when the food-processing machines are contaminated. Kat plays a vital role in the success or failure of the "Passage" through space.

Chief Tyrol and his wife Cally become trapped in a malfunctioning airlock. Adama remembers his late wife Carolanne as he marks his wedding anniversary. His relationship with President Roslin continues to become more friendly and personal.

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.

The Cylons learn that the Final Five are in the Colonial fleet. Some of the Cylons want the Cavil model to stop lobotomizing the Raider ships. Starbuck desperately tries to convince the others that the fleet is going the wrong way in their search for Earth.

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.