Deciding to use the thousand prisoners on a prison transport ship to mine the ice on the planet they've found, Galactica's plans are upset when a political prisoner onboard leads an uprising, taking hostages. He questions the legitimacy of Roslin's government and demands free elections to be held in the fleet.

Starbuck has been shot down over a barren moon, and must be rescued before she runs out of oxygen. Adama become obsessed with trying to save her even when all hope seems lost, putting the fleet at risk. Meanwhile, Starbuck finds the Cylon Raider she shot down, and tries to learn how to fly it so she can escape.

A humanoid Cylon straps himself with explosives and commits a suicide bombing in a crowded hallway on Galactica. Roslin and Adama are forced to publicly reveal that the Cylons now have models that look like humans, and a wave of paranoia spreads over the fleet as everyone starts being suspected of being a Cylon.

After Baltar has an argument with the vision of Number Six he sees in his head, a physical copy of Cylon model Number Six shows up in Galactica's CIC claiming to be a woman named Shelley Godfrey who has evidence that proves that Baltar has betrayed humanity...except that she's trying to frame him for an act of pre-attack sabotage.

A humanoid Cylon is captured in the fleet, a copy of the Leoben model, who claims that he has planted a nuclear bomb in the Fleet before he was captured. Starbuck is tasked with interrogating him, which soon becomes a battle of wills as Starbuck has her marines to torture the Cylon to try to break him.

After the interrogated Cylon gave Roslin the idea that Adama might be a Cylon, Roslin becomes suspicious of him. Unexpectedly, Colonel Tigh's estranged wife Ellen turns up alive in the fleet, apparently miraculously, raising the possibility that she might be a Cylon.

President Roslin has rebuilt a new Quorum of Twelve, the legislative branch of the government, but terrorist leader/political dissident Tom Zarek is elected as a member, and immediately motions that the Quorum vote to appoint a new Vice President, and runs for the office.

Galactica stumbles upon Kobol, the long-lost home world of humanity that the 13 Tribes came from, which legend says holds the only clues to the location of Earth. Roslin convinces Starbuck to steal the captured Cylon raider and return to Cylon-occupied Caprica with it to retrieve a religious artifact that will unlock the secrets on Kobol.

Infuriated that Roslin usurped his command by ordering Starbuck to steal the captured Raider, Adama decides that his only option is to storm Colonial One with marines and terminate her presidency. Starbuck reaches Caprica and finds the Arrow of Apollo in a museum, but she has to go through a copy of Number Six to get it.