Baltar learns from Caprica Six of their ability to project themselves and imagine different surroundings which leads him to wonder if he too is a Cylon. He has told the Cylons what he knows about the location of Earth and they dispatch a Basestar to investigate. In the end, the survey ship is infected with a virus killing everyone aboard. Aboard the Galactica, Lt. Gaeta has been reviewing Baltar's work in deciphering the map they recovered on Kobol. He too thinks he knows what it all means. Of greater concern however is the wedge between those who stayed with the fleet and those who were on the ground fighting the Cylons. Starbuck and Colonel Tigh in particular are quite vocal in complaining about those who stayed behind and it's left to Admiral Adama to lay down the law.

When a group of ill Cylons from the infected Basestar is brought to Galactica, Lee discovers a way to solve the Cylon problem forever - by destroying the whole Cylon race. Meanwhile, D'anna's acts to discover if Baltar is reliable will forge an unusual relationship.

A figure from Adama's past returns to haunt him. His return raises questions about why the Cylons launched their initial attack against the Twelve Colonies.

The Colonial fleet makes a harrowing journey. Kat plays a vital role in the success or failure of the passage.

The crew of Galactica makes a stop at the barren Algae planet.

Starbuck (Katee Sackhoff) and Laura Roslin (Mary McDonnell) face off with a gun between them, Lee Adama (Jamie Bamber) says goodbye to the Galactica, violent conflict breaks out between the seven models aboard Cylon Basestar, and Gaius Baltar (James Callis) is directly pulled into the "Final Five" situation.

A vicious injury ends the mutiny attempt aboard the Demetrius, Kara leads her crew to the Cylon rebel's Basestar, and Roslin begins to understand Gaius Baltar's appeal to his followers. Meanwhile, Anders attempts to secretly find answers to his purpose as a member of the Final Five.

A shaky alliance between the Colonial Fleet and Cylon rebels is put to the test when the two groups combine efforts to take out a Cylon "Resurrection Hub". Meanwhile, Athena loses control when Hera becomes unnaturally drawn to Natalie.

The Hybrid keeps jumping the basestar, and Roslin has visions. The three, D'Anna, is un-boxed. Humans and Cylons engage in a battle to destroy the Resurrection Hub. Baltar is badly wounded and Roslin has to decide whether or not to help him.

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.

As conflicts reach a climax, Cylons and humans face a stark choice.