While Commander Adama leads the rag-tag fleet of ships to the planet Kobol, where he hopes to find clues of Earth's location, the Viper pilots contract a disease, making it necessary for the women to take on fighter patrol duties. But the traitor Baltar leads the Cylons in an attack on the Galactica.

Baltar attempts to lure Galactica into range of a gigantic pulsar cannon. Adama becomes aware of the trap and sends in a team of commandos to destroy it.

Apollo and Starbuck lead a group of convicts on a possible suicide mission to destroy the cannon, which is located on an icy planet.

Starbuck crashes on the planet Trillion, where the Cylons have destroyed all the humans except for a band of children, who have become warriors to save their enslaved father.

While on patrol, Apollo and Starbuck encounter the supposedly lost Battlestar Pegasus, commanded by the living legend, Commander Cain.

The brash Commander Cain insists that the Galactica join in on a frontal attack on the Cylons -- an attack that Adama believes would be a suicide mission.

While the fleet is plagued by glowing lights that constantly fly past them too fast to be followed, Apollo, Starbuck, and Sheba find the remains of a shipwreck, with a mysterious and seemingly all-powerful being named Count Iblis, who helps them capture Baltar.