During a seemingly hopeless battle, Kara Thrace appears in a pristine Viper, claiming that she has been to Earth and can lead the Fleet there -- but the terminal Laura Roslin believes otherwise. Meanwhile, four of the so-called Final Five are forced to tackle the repercussions of their newfound nature, while Gaius Baltar discovers he has a commune of nubile female cultists who believe him to be an agent of the "one true God".

Gaius Baltar causes intense unrest within the fleet when he begins to openly promote belief in the Cylon god. Colonel Tigh, Galen Tyrol, and Tory Foster argue over how far they should go to ensure their secret is not revealed.

When a Heavy-Raider manned by Leoben Conoy docks aboard the Demetrius, confrontations form between the crew over the possibility of a truce with Cylon rebels, while Starbuck puts her trust in an old enemy.

D'Anna demands that the four Cylons in the fleet be sent to the basestar. Only Tory goes, while the remaining three are suddenly drawn to Kara's Viper by the music. The route to Earth is finally found.

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.

The Fleet refuses to cooperate with Cylon engineers and Adama decides to put an end to it. He sends the Quorum a message stating that unless they wish to join Zarek in the cell, they get their people in line. However, Gaeta has already freed Zarek with the help of other would-be-revolutionists. They allow Zarek to leave Galactica on a raptor. He lands on Colonial One and enters a gathering of the Quorum. Meanwhile, Anders gets ambushed and captured. At the CIC, Gaeta cleverly manipulates everyone else until the time is at hand for the revolution to begin.

Ellen and Boomer travel to the Galactica. Saul is entranced at the sight of his wife while Adama puts Boomer in the brig. Ellen is not so pleased when she learns that Caprica Six is pregnant by Saul. Her interference and jealousy leads Six to have a miscarriage. Sam Anders survived the operation but now seems to be brain dead. Ellen is disappointed that the Final Five cannot be completely reunited. By majority vote, the Five agree that they will go off on their own, leaving the Colonial Fleet behind. Adama has agreed to have the cracks in the Galactica's hull repaired using a Cylon living resin.

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.