In a distant part of the universe, a civilization of humans live on planets known as the Twelve Colonies. In the past, the Colonies have been at war with a cybernetic race known as the Cylons. 40 years after the first war the Cylons launch a devastating attack on the Colonies. The only military ship that survived the attack takes up the task of leading a small fugitive fleet of survivors into space in search of a fabled refuge known as Earth.
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 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.
Kara Thrace seeks her own path in the search for Earth while the Cylons face the threat of sentient Centurions. A member of Galactica's 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.
President Roslin faces challenges as the Colonials plot with Cylon rebels to destroy a Resurrection Hub.
With President Roslin missing along with the cylon base ship a new president must be decided on. Galactica goes on a search for the missing base ship and the Galactica crew members that were on board.
Colonial Viper pilots plan an attack on the Resurrection Hub with their Cylon rebel allies.
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.
Tigh and Number Six take their first glimpse at their unborn child, Tyrol offers Adama Cylon technology in return for his fellow Cylons properly reintegrated into the fleet, and an attempted coup leads to a costly struggle to maintain civility.
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.
As Sam Anders recovers from his head injury onboard the Galactica, he begins to remember events from ancient Earth. 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 feels lost while she struggles to cope with Sam's continued coma, meanwhile Boomer faces charges of treason from the Cylons onboard the base ship who blame her for voting against her model during the civil war causing the deaths of thousands of Cylons.
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.
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 liason 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.
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.D'Anna Biers/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 (D'Anna Biers) vows to put a final end to the New Caprican experiment.
Tyrol participates in the Circle, a secret tribunal on Galactica that tries and convicts in absentia those accused of collaborating with the Cylons during the Occupation.The death sentences--administered without the knowledge of Roslin or Adama--begin to weigh on Tyrol's conscience.Baltar faces a similar jury among the Cylons, who must decide whether he is allowed to stay with them.
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.
A figure from Adama's past returns to haunt him. His return raises questions about why the Cylons launched their initial attack against the Twelve Colonies.
Adama stages a boxing tournament on the Galactica to help the crew relax. The competitive atmosphere sets off a brutal match between Kara and Lee. Flashbacks from New Caprica reveal the origin and nature of their dispute.
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.
Tyrol discovers the Temple of Five on the algae planet. The temple may hold the Eye of Jupiter, which is believed to show the way to Earth. The Cylons take a keen interest in the discovery.Athena learns that her baby, Hera, may still be alive. Lee relies on Anders to help build civilian support for the protection of the Eye. His relationship with Kara complicates matters.
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.
Now onboard Galactica, Baltar faces charges of treason. He contemplates suicide with the help of Number Six. Questions remain about his true identity. Is he a Cylon or isn't he?Apollo shows off the new drinking establishment on Galactica, Joe's Bar, to Tyrol. Apollo thinks about Kara and wonders whether his marriage to Dee is worth saving.
The Sagittarons allege that a doctor is discriminating against them. As Helo investigates, he becomes concerned that the doctor may even be murdering patients. Meanwhile, Athena unwittingly brings Hera to the doctor for treatment.
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.
Amid a heated labor dispute, Tyrol asks the imprisoned Baltar for advice. Seelix becomes involved after she is turned down for flight training.
Kara continues to have dreams about Leoben Conoy and the mandala she painted at her old apartment on Caprica. While on patrol in her Viper, she encounters a Cylon Heavy Raider.When Tyrol cannot verify Kara's claim that the Cylon ship struck the Viper, Admiral Adama and Lee become concerned about her mental stability.
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.
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.
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.