The secret source in the administration has provided Tyrol with a list of all humans scheduled for extermination. Tyrol's wife Cally is on the list and he sets off to rescue her. Sharon Agathon has made it safely to the planet but they are ambushed by Cylons lying in wait. They realize they were betrayed and Anders finds damning evidence that points to the identity of the traitor. D'Anna Biers has been having strange dreams of late and an oracle tells her that the child Hera is alive and she will hold her in her arms. Roslin meanwhile assigns a squad of men to protect the child at all costs. The Admiral sends the Pegasus away with the few remaining civilian ships to continue the search for Earth.

The attack to rescue everyone on New Caprica begins. The Galactica encounters four rather than the expected two Cylon Basestars. The end appears in sight but they get help from a welcome but unexpected source. On the planet below, Tyrol and Anders lead the attack to free everyone from the prison. Anders finds Starbuck but she won't leave without Kacey. Her successful return to the Galactica results in mixed emotions. Colonel Tigh must decide what to do about his wife Ellen after she admits to giving the rendezvous coordinates to the Cylons. Hera doesn't make it off the planet.

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.

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

The Cylons descend upon the re-supply mission as the Chief races to decipher the markings in the temple believed to hold The Eye of Jupiter, a sacred icon that is believed to contain a map to Earth.

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.

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.