Baltar goes on trial for his life, and it affects everyone from Lee on up to the president.

Coincidences creates new alliances aboard Galactica.

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.