The crew of Galactica is exhausted after 237 consecutive jumps in intervals of 33 minutes and 132.25 hour without sleep to escape from the Cylons. When Galactica is contacted by the Olympic Carrier, a vessel with more than 1,300 persons, Commander William Adama and are advised that there is a traitor on board. However, Dr. Gaius Baltar convinces both leaders that the Olympic Carrier is a menace to the refugee fleet led by Galactica.
President Roslin arrives on Galactica as Boomer's Cylon side asserts itself, forcing her to sabotage Galactica's water supply against her will. A series of explosions leads to the loss of 60% of the water reserves and Commander Adama is compelled to introduce rationing and begin a search of nearby planetary systems for any H20 deposits.
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.
There's a party on Galactica's flight deck as Flat-Top just had his thousandth landing. Something goes terribly wrong however when a drone accidentally goes off and explodes in a group of pilots. 13 are dead. During the ceremony Kara Thrace starts thinking about her dead fiancée Zak Adama. And those memories even get clearer when Adama orders her to start training new pilots. She seems very uncomfortable in doing so. The favor she did for Zak by letting him pass basic flight seems to bother her more and more. Angrily she stops training pilots after just one day. ...
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.