The human survivors aboard the Battlestar Galactica struggle to outwit the pursuing Cylons, moving to a different location every 33 minutes, only to be immediately found by the Cylons.
Sharon Valerii awakens within the tool room, but has no memory of how she got there. Wet and confused, she finds explosives in her bag, a discovery which soon comes back to her when the water tanks onboard explode, which could impair the whole fleet.
Lee's proposal to have prisoners gather water from the surface of an ice-covered moon goes awry when a convict rallies a group of his prison peers to stage an uprising and hold some of the ship's officers hostage.
When a group of Galactica's fighter pilots are killed in an unforseen accident, Kara has no choice but to give instruction to a new batch of pilots, an activity which forces her and Lee to revisit another past tragedy.
Adama and Lee jeopardize the fleet's safety when they allocate too much of its resources to find Kara after her disappearance in the midst of hostile fire.
The existence of Cylons with a human appearance is confirmed by Adama after an attack by one of them which costs several innocent lives, but the possibility still exists that more could be lurking among Galactica's crew.
Baltar is accused by a vindictive, estranged Number Six of abandoning the humans in favor of helping the Cylons. Number Six, now in a different, human form, then sets her sights on Commander Adama. Meanwhile, Kera begins to recuperate from her wounds, while Sharon faces two different conflicts, one on Cylon-ridden Caprica, the other aboard the Galactica.
Kara is emotionally conflicted when she is assigned to torture a Cylon prisoner in order to gain information about a potential bomb hidden among the Galactica's fleet.
President Roslin begins to have suspicions that Commander Adama is really a Cylon. Meanwhile, Col. Tigh's ex-wife returns and tells him she wants the two to get back together.
As the ships become in dire need of fuel, Commander Adama decides that the fleet must mount an attack on a tylium mine operated by the Cylons.
Just as Zarek gets himself a vice presidential nomination, a killer is discovered aboard the decadent Cloud Nine ship, but the implementation of democracy ends with a murder and a tension-filled political appointment.
The Galactica makes it to the hospitable planet, Kobol. Meanwhile, Baltar, Lee, and Kara realize they are all ensconced within an uncomfortable triangle.
The Galactica fleet prepares to engage the Cylons in battle for control of Kobol. Meanwhile, the President orders Starbuck to retrieve the newly-discovered Arrow of Apollo, but tensions flare up between her and Adama, prompting him to call for her arrest.