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.
The Cylons realize that their Raiders now refuse to attack the Colonial human fleet after one of the Raiders identified a Final Five Cylon among the humans. The decision to lobotomize the Raiders leads to tension among the human-form Cylons.
Starbuck is desperate to stop Galactica as it continues to jump away from the Ionian nebula. Apparently alone in her quest, she finds an ally in an unexpected place.
Kara Thrace seeks her own path in the search for Earth as the commander of a lone freighter. The Cylons face the threat of the newly sentient Centurions unleashed by Natalie, a copy of Number Six.
On the Galactica, a member of the crew learns a dark secret about a loved one.
Gaius Baltar sets off a debate on religious freedom when he promotes his belief in a single God.
Specialist Tyrol continues to sink into despair after his recent loss. He becomes curious about Gaius Baltar's sermons and the following he has attracted.
The crew of the Demetrius grow concerned about Kara's mental stability as an old enemy arrives with a tempting offer.
The dying President Roslin and the aggressive Viper pilot Kara Thrace try to accept the new terms of the relationship with the Cylons.
Adama and the fleet are presented with the proposed alliance with the Cylon rebels. Natalie offers an enticing prize to win Roslin's acceptance, but trust doesn't follow so easily.
After President Roslin's disappearance, Admiral Adama is reluctant to recognize Tom Zarek as the new president. Lee realizes that his father will never accept Zarek so he seeks the assistance of attorney Romo Lampkin in finding another candidate.
Meanwhile, Adama continues the search for the missing Cylon base ship, and President Roslin.
Colonial Viper pilots plan an attack on the Resurrection Hub with their Cylon rebel allies. Meanwhile Laura Roslin struggles with her morals and ethics as she makes a momentous decision.
D'Anna holds President Roslin and other Colonials hostage in order to draw out the Final Five from the Colonial fleet. Col. Tigh believes he has the solution to end the standoff.
Kara struggles with the foreboding prediction of the Cylon Hybrid, while Adama and the Colonial fleet face despair over their shocking discovery.
Admiral Adama wants to use Cylon technology to help the fleet find a new permanent home, but not everyone agrees with his plan.
Adama continues with his plan to use Cylon drive technology on Colonial ships. The closer ties between the rebel Cylons and the humans sets off a unhappy uprising in the fleet.
President Roslin seeks refuge on the Cylon base ship after Tom Zarek and Lt. Gaeta take control of the Galactica. Gaeta is determined to break away from Adama's policy of cooperation with the Cylons but even he is disturbed by Zarek's unhappy actions.
As Sam Anders recovers from his head injury onboard the Galactica, he begins to remember events from ancient Earth. Meanwhile, the Final Cylon struggles with the fallout from the Final Five's former plans. One of the humanoid Cylons vows to get revenge for being created in the image of Man. Tyrol informs Admiral Adama about the extensive structural damage on the Galactica.
Ellen escapes from Cavil only to face a momentous choice regarding the 13th Tribe and the Final Five Cylons.
Kara befriends a piano player who reminds her of her father. She also receives a mysterious drawing from young Hera Agathon. "Boomer" faces punishment for her support of Cavil in the Cylon civil war. She reconnects with Chief Tyrol and shares her visions of a peaceful life on Picon. However, her life on Galactica is much less tranquil.
The rebel Cylons and the Colonial humans react to Hera's kidnapping while the physical condition of the Galactica continues to deteriorate.
With Galactica on the verge of falling apart, Admiral Adama readies the ship for what could be its final mission, as Baltar's Six warns that humanity's final chapter is near.
Destinies that have long been in the making are finally decided when Galactica mounts its final mission in an effort to rescue Hera from the Cylon colony.