Lingering feelings of rage lead Saul Tigh and Kara Thrace to cause problems aboard Galactica between the survivors from New Caprica and those who stayed with the fleet during the Occupation. Baltar assists the Cylons in an attempt to stay alive and uncovers details about Cylon civilization. A Cylon baseship falls victim to a mysterious disease.

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 faces starvation when the food-processing machines are contaminated. Kat plays a vital role in the success or failure of the "Passage" through space.

Tyrol discovers the Temple of Five on the algae planet. The temple may hold the Eye of Jupiter, which is believed to show the way to Earth. The Cylons take a keen interest in the discovery. Athena learns that her baby, Hera, may still be alive. Lee relies on Anders to help build civilian support for the protection of the Eye. His relationship with Kara complicates matters.

The Cylons learn that the Final Five are in the Colonial fleet. Some of the Cylons want the Cavil model to stop lobotomizing the Raider ships. Starbuck desperately tries to convince the others that the fleet is going the wrong way in their search for Earth.

The dying President Roslin and the aggressive Viper pilot Kara Thrace try to accept the new terms of the relationship with the Cylons.

President Roslin faces challenges as the Colonials plot with Cylon rebels to destroy a Resurrection Hub.

Colonial Viper pilots plan an attack on the Resurrection Hub with their Cylon rebel allies.