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.
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.
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.
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.
Amid a heated labor dispute, Tyrol asks the imprisoned Baltar for advice. Seelix becomes involved after she is turned down for flight training.
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.
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.
Now on board 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
