With Adama critically wounded, Colonel Tigh is now in a position he never wanted to be in: commander of Galactica. To make matters worse, an error in jump calculations seperates the ship from the rest of the fleet. Meanwhile, as Starbuck faces Sharon's Cylon identity and her relationship with Helo on Caprica, the crew of the downed Raptor try to stay alive on Kobol.

The success of reuniting with the fleet is short-lived as Galactica has been boarded by a party of Cylon Centurions, while Baltar's visions on Kobol are becoming more disturbing.

Tigh feels further stress in his position when he must confront the Quorum of Twelve over Adama's decision to imprison President Roslin. On Kobol, the survivors struggle to ensure rescue when they find the Cylons building an anti-aircraft battery.

As Tyrol is jailed for suspicion of being a Cylon, Tigh's declaration of martial law is causing unrest in the fleet, prompting Lee to help plot Roslin's escape. Elsewhere on Caprica, Helo and Starbuck meet a group of resistance fighters led by pyramid players.

When Kara is wounded, she wakes up in a hospital where she discovers an unsettling part of the Cylons’ plans. Now up and about, Adama faces to pick up many of the pieces left scattered since his absence. Among those is the increased divison of the fleet due to their loyalty to Roslin.

Adama tries to carry on commanding the remains of the fleet, even with the loss of material and people. With the Arrow of Apollo in their possession, Roslin and others set foot on Kobol to embark in the quest for the tomb of Athena.

Roslin and the others are still plagued by the dangers surrounding them on Kobol. This is especially troubling with the Cylon Sharon as their guide. When Adama joins in his goal to reunite the fleet, the mistrust of her is doubled, as is the danger. Baltar, meanwhile, has doubts that the Number Six he sees is just a chip in his head.

The actions of Tigh’s temporary command has resulted in much negative perception of the military. In order to alleviate this contempt, reporter D’anna Biers is allowed full access to Galactica and its people to allow the fleet to see the human face of those who protect it.

Morale among the crew is beginning to wear thin. Their only rallying point of hope is the building of a fighter from scratch initiated by Chief Tyrol, a project he uses to help himself cope with the abruptly ended relationship with Sharon. Meanwhile the current Sharon being held on Galactica is the target of much of the crew's resentment, though she maybe their only hope when a virus threatens to usher in a Cylon attack.

Everyone on Galactica is excited when they find another lost survivor of the Cylon attacks: the battlestar Pegasus. Soon, however, things begin to sour when the crew finds itself under the rule of Helena Cain, an admiral who is more stern than Adama.

When Kara returns from an unauthorised recon mission, Adama and Cain decide to put their conflict on hold long enough to destroy a valuable Cylon asset.

As the two battlestars prepare to destroy the Cylons' resurrection ship, Adama and Cain ready their people to carry out their orders while Baltar comforts the Pegasus' Cylon prisoner.

Roslin’s cancer pushes her to her final hours, as she looks back at her relationship with President Adar, and particularly a significant day on Caprica. During this time, a group of Cylon sympathisers threaten the safety of the fleet.

When Pegasus commander Jack Fisk is found murdered, Admiral Adama assigns Lee to investigate. Haunted by his near-death experience and memories of a lost lover, Lee uncovers a large black market organisation.

Galactica sends Vipers to protect mining units on an asteroid from Cylon Raiders. But one in particular, filled with rage and unwilling to die a permanant death, gives the pilots the most trouble. Questioning what she herself has to live for, Starbuck enters a competition with Kat to gun it down for good.

Adama’s reliance on Sharon for information is put to the test when a widow and three assistants take hostages on Cloud 9. With rumblings of a Cylon alive on Galactica stirring in the fleet, their demand is the Cylon they believe to be working towards their destruction.

Lee and Kara butt heads with the new commander of Pegasus after a Raptor team goes missing. He is determined to rescue his men, but he may very well be heading his ship into a trap. Meanwhile, a young girl’s desire for an abortion is a political issue that weighs heavier on Roslin as a moral dilemma.

The consciousness of two Cylon models have been downloaded into new bodies and made celebrities for their success: the Number Six who seduced Baltar before the attack on the Colonies and the sleeper agent from Galactica known as Boomer. However, neither are accepting of their status. Elsewhere in the Colonial fleet, a decision must be made over what to do with Sharon’s baby for fear of what the hybrid child might mean to the Cylons.

While on a major rescue mission to Caprica, an accident leads to the discovery of a habitable planet. And since it is also clouded from Cylon detection, Baltar uses the hope of settling the fleet on its surface as a major platform to help boost his campaign against Roslin.

As the fleet vote for their new leader, a shift in the Cylons' own leadership offers humanity a reprieve. However, Roslin is certain that Baltar's presidency will bring with it only disaster, and is prepared to do whatever it takes to prevent it.