As Baltar's trial comes to a conclusion, key members of the fleet discover that they may be the Final Five Cylons. Tigh attempts to decipher the strange music he is hearing in his head, while a Cylon fleet approaches.

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.

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

The struggle between Adama and Cain is temporarily put on hold while the two Battlestars combine forces for an assault on the Cylon Resurrection Ship. Apollo faces a momentous decision and Baltar takes an interest in Gina, the Cylon prisoner.

When Commander Adama learns that Kara disobeyed orders and Jumped to Caprica on orders from President Roslin, he demands the president's resignation, with the implied threat of a military coup. Roslin refuses his demand and sparks a confrontation.

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.

When Baltar wins the vote, Roslin considers stealing the election because she believes he is a Cylon collaborator.

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.

In the wake of the Cylon sneak attack, the ragtag fleet of human survivors is forced to play a deadly game of cat-and-mouse with their pursuers. Every 33 minutes, they make a jump to a new location. And every 33 minutes, the Cylons manage to find them. The pilots are on the brink of exhaustion, relying on artificial stimulants to keep fighting, and the civilians are beginning to doubt the leadership of Commander Adama and President Roslin.

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.

As its fuel supply dwindles, the fleet must seek out a new supply of tylium ore or risk becoming sitting ducks to any Cylon attack. A recon patrol finds an asteroid full of the fuel, but there's a catch — the Cylons have found it first and established a heavily guarded refining plant.

After Boomer's consciousness is downloaded into a new body following her death, she struggles with her new life on Cylon-occupied Caprica. Number Six is asked to help Boomer adjust to her new role in Cylon society.

Kara struggles with the foreboding prediction of the Cylon Hybrid, while Adama and the Colonial fleet face despair over their shocking discovery.

While flying a supply patrol, Crashdown and Sharon Valerii discover a bountiful planet that can support human life. Indeed, it might be Kobol, the legendary "home of the gods." The discovery prompts Commander Adama to send a ground team to investigate; it also gives new life to President Roslin's belief that she is a tool of destiny and that this discovery, like her rapidly spreading cancer, is part of an ancient prophecy.

Adama heads to Kobol to find Roslin, reassembles the fleet and heads down to Kobol himself to find the presidential party in search of the "Tomb of Athena" which allegedly leads to Earth. Apollo hangs out with Starbuck , Zarek tries to keep his cronie off plotting with Boomer who is unaware of tension building between Helo and Tyrol.

Baltar's trial testimony threatens the very stability of the fleet. Lee assists Romo Lampkin in Baltar's defense. Some in the fleet begin to feel that Baltar is divine. Though he dismisses such beliefs, Number Six suggests that the followers may know more about his true nature than Baltar does himself.

Colonial Viper pilots plan an attack on the Resurrection Hub with their Cylon rebel allies.

Adama and the Galactica crew stake the survival of the human race on their plan to rescue Hera from the Cylon colony in this, the series finale.

When Lt. Kara Thrace goes missing in action after encountering a Cylon patrol while on a training mission, Commander Adama feels responsible — especially in light of her recent admission that she blames herself for his son Zak's death.

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.

Sharon informs Adama that the Galatica has been infected with a computer virus that is tampering with the basic ship functions and is scanning them for weaknesses. All this is preparation for a major assault by the Cylon Raiders. So with the clock ticking, Commander Adama must pull himself together and decide: Can he trust Sharon?

Tigh, Tyrol and Anders lead the Resistance on New Caprica to increasingly deadly attacks against the Cylons. Kara finds herself trapped in a new life with Leoben Conoy, and Duck makes a fateful decision. Meanwhile on Galactica, Adama struggles with the question of whether to return to New Caprica to mount a rescue attempt.

Adama plans to return to New Caprica and drop off a surprising person to act as a liaison between Galactica and the Resistance. Tigh's insistence on the use of suicide bombers and ever escalating violence stuns even the fellow leaders of the Resistance. Eventually, the suicide bombings cause the Cylon occupiers to crackdown on their human subjects.

D'Anna/Number Three squares off against Adama over the Temple of the Five. Athena asks for Helo's aid in her plan to rescue Hera. On the algae planet, Apollo orders Dee to leave her defended position in order to save Kara. Anders helps Apollo to hold off the Cylon Centurion attack. Another copy of D'Anna finds the Temple and continues her search for the identities of the Final Five. Her messianic complex begins to concern the other Cylons.

During the Cylon attack, Sam Anders has a strange encounter with a Cylon Raider. The crew of the Galactica view Starbuck's return with suspicion and doubt. Gaius Baltar takes refuge with a group of women who believe he has the power to heal others.