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.

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

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.

Baltar plays a game of cat and mouse with Adama and the President, thinking they will kill him once they've gotten out of him what they want to know. Lee deals with his feelings for Kara, while struggling to hang on to his marriage.

Adama considers Saul and Tyrol's suggestion that the Fleet should integrate Cylon jump technology since it will triple the distance they will be able to cover before they run out of fuel. But the Cylon's condition is that they will be allowed to join the Fleet, for safety against Cavil, who's still out there. Ultimately, the decision is up to President Roslin, but Zarek calls the Quorum and gets them to carry the motion that no Cylon be allowed aboard any Colonial vessel unless permitted by the ship's captain. Tyrol learns from Dr. Cottle that Cally had their child tested and the results indicated that Tyrol is not the father - therefore the child is fully human. Roslin starts her climb up from the depths of despair she had fallen to soon after the Fleet found Earth.

Eighteen months ago: Saul poisons Ellen, who then finds herself downloaded into a new body aboard a Cylon Base Star, with a single Centaurion keeping watch over her. After the initial shock, she has a revelation as she remembers things she had forgotten. Present Day: Dr. Cottle is operating on Anders, who has a bullet lodged in his brain. Anders starts to remember things he had forgotten. Eighteen months ago: Cavil comes to see Ellen, who calls him John, because that's his "real" name. Cavil says he hates that name. John was the first Cylon model *Ellen* created. She also created seven others. So, there are actually only *eight* Cylon models and the "Final Five" are actually copies of humans who lived 2,000 years earlier and, together, created Resurrection, which allowed them and the Cylons to download. Number Seven, Daniel, was a favorite of Ellen. Jealous, John sabotaged the process of using Resurrection on Daniel, making him unique. John and Ellen start a months-long philosophical and ethical argument on Cylon - human interaction. John says he started the genocide of humankind because his "forebears on the Centaurion side of the family were the slaves of humanity." And he wants justice for that. Present Day: Anders tells Starbuck that he has seen "everything" and needs Kara to get "the others" - Galen, Tory, Saul and Ellen to his bedside. Anders says he remembers everything and knows why they have come all the way to Earth... Adama reinstates Tyrol as a Chief of Engineering. Tyrol starts inspecting the damage Galactica has taken during their journey. But he is not prepared for what he finds and Adama is not prepared for what Tyrol suggests as a repair method.

With Hera now likely in the hands of John Cavil, Admiral Adama sends out search teams to locate The Colony, the Cylon home world if you will, that Ellen Tigh says is the only place she imagines she could be. Adama reluctantly comes to the conclusion that the Galactica has reached the end of its days. He orders all repair activities halted and decides to strip the ship and share everything that is salvageable with the rest of the fleet. Starbuck meanwhile shares with Gaius Baltar what she found on the uninhabitable Earth. He subsequently - and quite publicly - proclaims her to be an angel.

The Colony is located sitting on the edge of a black hole with only one point of entry in what is a very large debris field. Knowing that the Galactica has reached the end of the line, Admiral Adama asks for volunteers to mount a raid on the Cylon base, realizing it may be the ship's last jump. In flashbacks prior to the Cylon invasion, key moments in the lives of several of the crew are presented. These include include the first time Kara Thrace and Lee Adama meet; Admiral Adama's struggle with his decision to retire from the colonial fleet; Gaius Baltar's relationship with his father and his developing relationship with Caprica Six; and Sam Anders discussing the motivation behind his professional sports career.

A stripped down Galactica attacks the Cylon's Colony ship in the hopes of rescuing Hera. The meaning of the shared dream in the Opera House on Kobol is revealed. Sam Anders is moved in his Hybrid tank to the CIC in the hopes that he will be able to assist the combatants. Their mission complete, Admiral Adama orders Starbuck to pick a destination - any destination - to which the ship can jump to get out of there. With that, the meaning of the tune and the musical notes are explained. Having successfully jumped, the old Galactica has truly reached the end of it's life. A planet capable of sustaining life is found and Lee Adama makes a radical proposal for the future of humankind. In a flash forward far into the future, Hera's importance to the human race is revealed.