The Cylons are attacking the fleet every 33 minutes. The fleet has barely enough time to jump away, and this has been going on for days, and everyone is exhausted. On one jump, they leave behind the Olympic Carrier ... and the Cylons don't appear. Three hours later, the Olympic Carrier turns up, claiming trouble with its FTL engines. 33 minutes later, the Cylons appear. The President gives the order to destroy it. Meanwhile, back on Caprica, Helo is being pursued by Cylons, until he is rescued by ... Boomer.
Boomer wakes with no memory of where she has been, and a detonator in her duffel. She discovers six others missing. Then the Galactica's water tanks are ruptured. A desperate race is on to find a planet with water to replace it.
The prisoners on the convict ship are invited to volunteer for water mining. Instead, led by notorious terrorist Tom Zarek, they rebel, and take hostages, calling for elections. President Roslin refuses to negotiate. Commander Adama sends in the Marines. Apollo negotiates a compromise, insisting on elections in 7 months, when the President's term legally ends.
An accident kills many pilots. Commander Adama asks Starbuck to train new pilots. She flunks them, being unwilling to pass anyone after having passed Zach Adama, leading to his death. The Commander learns of this. The trainees are reinstated, and on a training flight, they meet Cylons. Starbuck is forced to eject, and left drifting towards a moon... Meanwhile, on Caprica, Helo and another Boomer have found a bunker of supplies...
An injured Starbuck has landed on the gas giant moon, and found a crashed Cylon fighter. She teaches herself to fly it. On Galactica, they are frantically searching for Starbuck, but once they know her oxygen must have run out, the President tells them to call off the search. But just before they jump, they see a Cylon fighter approaching. Apollo goes to intercept, but Starbuck has written her name on its wings. Meanwhile, on Caprica, Helo and Boomer are attacked by Cylon robots, and Boomer goes missing...
A suicide Cylon bomber kills several people on Galactica, and the fact that Cylons can look human is made public. In the following investigation, a crew member lies to cover for Chief Tyrol's affair with Boomer, and is stripped of rank and sent to the brig. The Chief breaks off his relationship with Boomer. Meanwhile, on Caprica, Helo "rescues" Boomer from Cylon robots.
Number Six appears as a real person, and accuses Gaius of treason. It's looking bad for him, but eventually he's cleared, and is more popular than ever. Starbuck exits sickbay to help the Chief study the captured Cylon fighter. Meanwhile, on Caprica, Helo and Boomer make out.
Leoben Conoy, a Cylon, is captured, and Starbuck is sent to interrogate him. He claims he has planted a nuke on one of the ships, due to go off in about 8 hours time. President Roslin talks to him, and he tells her there was no nuke. She orders him spaced. On Galactica, Boomer demands that Gaius uses his Cylon test on her -- it comes up positive, but he lies to her. Meanwhile, on Caprica, Boomer disobeys a Cylon command to keep Helo in the forest.
Commander Adama discovers Colonel Tigh's wife Ellen on another ship, fit and well. He's concerned she might be a Cylon -- and even more concerned that she might not, given her reputation. Gaius's test proves negative -- but he tells Six that from now on, all his tests will. Meanwhile, on Caprica, Boomer and Helo keep running.
The fleet is desperate for fuel, and find an asteroid rich in the ore, but with a Cylon base present. The still convalescent Starbuck comes up with an attack plan, executed by Apollo, relying on Gaius identifying the critical part of the facility. President Roslin has a vision of 12 snakes, in line with an ancient prophecy about a great leader. Meanwhile, on Caprica, Boomer is sick.
President Roslin calls a government meeting on colonial day. Zarek, the prison ship rebel leader, is elected as the Sagittarius representative, and Gaius that for Caprica. Zarek calls for a vice-presidential election, and is nominated. Starbuck captures a potential assassin. Roslin asks Gaius to stand for vice-president, and he is elected. Meanwhile, on Caprica, Boomer and Helo near the Cylon base, and Helo sees another Number Six, and realises there may be clones. Then he sees a Boomer clone. His Boomer kills it to save him, but he runs.
On a scouting mission, Boomer discovers Kobol, the planet from which the exodus of the 13 tribes happened 2000 years ago. President Roslin has a vision of it as it was. She asks Adama for the captured Cylon Raider to be sent to Caprica to get the Arrow of Apollo, to fulfil one of the prophecies that will lead them to Earth. He refuses. She then asks Starbuck, telling her Adama lied about knowing where Earth is. An exploration team, including gaius, crash on Kobol, and are trapped there by a huge Cylon mothership. On Galactica, Boomer shoots herself, but does not kill herself. Starbuck steals the raider, and jumps with it. Meanwhile, on Caprica, Helo shoots Boomer, but does not kill her.
When Adama discovers Roslin set Starbuck after the arrow, he orders her to be arrested. On Kobol, the shuttle team, including Chief Tyrol and Gaius, await rescue. On Caprica, Starbuck finds the arrow, and is attacked by Six. Helo and Boomer discover the fight just as Starbuck and Six plunge off a wall, killing Six. Starbuck tries to kill Boomer, but Helo stops her, because Boomer is pregnant... Meanwhile, on Galactica, Adama sends Boomer on a mission to nuke the Cylon mothership. She succeeds, but discovers that she is a Cylon clone. Down on Kobol, Six leads Gaius to his destiny. During the arrest of the President, Apollo mutinies, standing up for democracy. But the President refuses to allow blood to be shed, and surrenders, and is put in the brig... Adama congratulates the returned Boomer on her successful mission, and she shoots him...