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When an old enemy, the Cylons, resurface and obliterate the 12 colonies, the crew of the aged Galactica protect a small civilian fleet - the last of humanity - as they journey toward the fabled 13th colony, Earth.

Following the destruction of the Twelve Colonies of Kobol by the Cylons, a rag-tag fugitive fleet of the last remnants of mankind flees the pursuing Cylons while simultaneously searching for their true home: Earth.

A two-hour Battlestar Galactica special that tells the story of the Battlestar Pegasus several months prior to it finding the Galactica.

When the initial Cylon attack against the Twelve Colonies fails to achieve complete extermination of human life as planned, twin Number Ones (Cavils) embedded on Galactica and Caprica must improvise to destroy the human survivors.

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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.

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. Meanwhile on Cylon-occupied Caprica Helo and Cylon-Sharon find a bomb shelter in a restaurant. It seems like a good place to stay for a while. There's food, water and anti-radiation medication in abundance.

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.

Apollo investigates the murder of one of the crew and falls for a young prostitute, whom he vows to save from the rogue ship dealing with the Black Market. As well as confronting the bad guys, Apollo has to confront some past mistakes.

President Roslin has rebuilt a new Quorum of Twelve, the legislative branch of the government, but terrorist leader/political dissident Tom Zarek is elected as a member, and immediately motions that the Quorum vote to appoint a new Vice President, and runs for the office.

The Cylon baby is finally born, leading to some political decisions being made. Meanwhile, the Cylons on Caprica contemplate life and humans when they meet up with a certain human from a previous episode. This story explores the Cylon world.

President Roslin, who is about to die, believes Sharon's baby is dangerous and orders it must die. Meanwhile, a terrorist group inside the fleet starts to ask for a peace negotiation with the cylons.

Journalist D'Anna Biers is making an item on the Gideon incident, when she's asked by Adama and Roslin to film daily life on Galactica.

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.

While Tyrol decides to start building a new fighter, the Cylon virus is rearing its ugly head again. Boomer says it means a large Cylon attack is imminent.

Tigh has problems with the responsibility of being a leader, president Roslin loses control without chamalla. The Kobol team discovers a Cylon battery.

Starbuck, Helo and Boomer bring back the Arrow of Apollo, but Boomer doesn't seem welcome. Commander Adama wants to keep the fleet divided and appoints a new CAG.

While Commander Adama tries to join Roslin's team on Kobol, Dr. Baltar's Number Six tells him he's crazy.

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.

While Dr. Baltar is behind in the polls for the election and tries desperately to turn things around, Starbuck is planning a mission to rescue Anders from Caprica.

The group on Caprica is under fire by the Cylons, but suddenly they stop. With only one ship's votes to be counted, Roslin is way behind in the elections.

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.

Gallactica meets Pegasus, and Adama's command is threatened when the captain of Pegasus outranks him. A joyous celebration turns sour at some of the secrets emerging out of the differences of the two crews, and Baltar meets a familiar Cylon prisoner aboard Pegasus.

Tigh's decision to impose martial law is protested in the fleet as well as on Galactica. On Caprica, Helo and Starbuck meet other humans.