Kara feels lost while she struggles to cope with Sam’s continued coma, meanwhile Boomer faces charges of treason from the Cylons onboard the base ship who blame her for voting against her model during the civil war causing the deaths of thousands of Cylons.
Ellen escapes from Cavil only to face a momentous choice regarding the 13th Tribe and the Final Five Cylons.
As Sam Anders recovers from his head injury onboard the Galactica, he begins to remember events from ancient Earth. The Final Cylon struggles with the fallout from the Final Five’s former plans. One of the humanoid Cylons vows to get revenge for being created in the image of Man. Tyrol informs Admiral Adama about the extensive structural damage on the Galactica.
President Roslin faces off against Tom Zarek and Lt. Gaeta as they try to take control of the Colonial fleet. Both the alliance with the rebel Cylons and Adama’s life are at stake.
Loyalties are made clear when Gaeta orchestrates a coup d’état of the Adama regime. Both prisoners and lives are taken as many of the fed up people work to take over Galactica.
Tigh and Number Six take their first glimpse at their unborn child, Tyrol offers Adama Cylon technology in return for his fellow Cylons properly reintegrated into the fleet, and an attempted coup leads to a costly struggle to maintain civility.
Kara struggles with the foreboding prediction of the Cylon Hybrid, while Adama and the Colonial fleet face despair over their shocking discovery.
D’Anna holds President Roslin and other Colonials hostage in order to draw out the Final Five from the Colonial fleet. Col. Tigh believes he has the solution to end the standoff.
Colonial Viper pilots plan an attack on the Resurrection Hub with their Cylon rebel allies.
With President Roslin missing along with the cylon base ship a new president must be decided on. Galactica goes on a search for the missing base ship and the Galactica crew members that were on board.