Besides having to deal with the loss of Kara Thrace, the crew of the Galactica is also charged with the security surrounding the trial of Dr. Baltar and his defense attorney, who is replacing one lawyer that has already been killed.

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

Coincidences creates new alliances aboard Galactica.

President Roslin's abduction by the Cylon Hybrid triggers a bitter power struggle within the Colonial Fleet.

Roslin is on board a raptor en route to the Rebel Cylon Base Star, but Gaeta has ordered to engage and destroy it. The marines have used a stun grenade on Adama and Tigh. Roslin manages to get a wireless transmission out for everyone to hear and learn what Gaeta has done. She and the others barely make it to the Base Star, where she convinces Tory and the other Cylons to use the Fleet as a cover in order to prevent Gaeta from attacking it. She also believes that Adama will be able to save the rest of the Final Four. Temporarily safe, the Rebel Cylons start voting on whether they should just jump away and count their losses. Adama is brought before Gaeta and Tigh is thrown to the brig with Caprica Six, Anders, Athena, Helo and their child Hera. Zarek comes aboard Galactica on Colonial One with the Quorum. At Gaeta's insisting, Zarek agrees to put Adama on trial for treason, with Romo Lampkin assigned as his defence lawyer. There's just one problem: The Quorum refuses to recognize Zarek's authority. However, Zarek is hell-bent on following his "The truth is told by those left standing" maxim. Only Tyrol, who's alone, and Lee, whose with Starbuck, are Galactica's last hope.

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.