Lt. Sharon Valerii wakes up soaking wet in the tool room with an explosive charge in her duffel bag. Shortly afterward, a mysterious explosion destroys all the port-side water tanks on Galactica, creating a crisis for the entire fleet. Sharon can't remember a thing, but all the evidence points to her as a saboteur. She confesses her concern to Chief Tyrol, but he can't believe she's responsible.

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.

A Cylon, who calls himself Leoben, is discovered on one of the ships in the fleet. Commander Adama sends Kara to interrogate him — or, rather, it. The Cylon tells Kara that he planted a nuclear device on one of the ships. Although she doesn't believe it, Kara passes on the warning.

When President Roslin calls an Interim Quorum of the Twelve Colonies, she discovers that democracy brings its ugly stepsisters — politics and deadly intrigue — to the party. Tom Zarek, the charismatic convicted terrorist, is elected as the delegate from Sagittaron and immediately proposes elections for the vice-presidency.

Democracy is brought back to the fleet and soon with it come hardball politics and potentially deadly intrigue.

Tigh imposes martial law and threatens to split the fleet as Lee works to free President Roslin and organize democratic resistance.

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

As President Roslin nears death, Dr. Gaius Baltar must be groomed for the worst case scenario. Roslin orders the death of Sharon's unborn child. A sabotaged Viper leads to an investigation that uncovers a movement of people seeking peace with the Cylons.

A woman takes hostages on Cloud Nine and demands that Adama turn over Sharon in order to avenge her husband's death at the hands of the Cylons.

Chief Tyrol is plagued by terrifying dreams and seeks the aid of a priest. Kara leads a rescue mission to Caprica. Roslin and Baltar go head-to-head in a presidential debate that changes dramatically with the discovery of a habitable planet.

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

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.

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.

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.

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.