The aftermath of a coup among the Cylons leads to further violence, Lee finds himself facing off against Roslin during his first meeting with the Quorum of Twelve as the new representative of Caprica, and Cally discovers the horrible truth about her husband Galen Tyrol. Meanwhile, Starbuck aimlessly searches for Earth with Anders and other Galactica officers.

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.

A shaky alliance between the Colonial Fleet and Cylon rebels is put to the test when the two groups combine efforts to take out a Cylon "Resurrection Hub". Meanwhile, Athena loses control when Hera becomes unnaturally drawn to Natalie.

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

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.

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.