The Galactica and the other remaining ships - with about 50,000 people aboard them all - are being pursued by the Cylons. They are forced to jump into hyper space every 33 minutes. Somehow, the Cylons know where they are going and appear exactly 33 minutes after the Galactica arrives. The crew hasn't slept for over 130 hours now and everyone is exhausted. They rejoice when they finally make a jump and the Cylons fail to appear at the 33 minute mark. They are also prone to make mistakes and realize they've left behind a ship, the Olympic Carrier, with 1300 passengers aboard. When the ship rejoins the fleet a few hours later, the Cylons again arrive 33 minutes later leading Adama to conclude that there are Cylon spies on board. President Roslin now faces a major decision. The identity of the the Cylon aboard the Galactica is revealed.

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.

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.

As the premiere for the second season unfolds, Adama lay dying leaving Tigh in command. Lee and Roslin have been sent to the brig. An emergency jump goes wrong leaving the Galactica alone in space without the fleet.

A Cylon virus is interfering with Galactica's power supply, while Cylon centurions are heading for crucial systems. Somehow they must be stopped.