The survivor count shown in the title sequence is 39,603
Felix Gaeta and Tom Zarek move to consolidate their insurrection in the fleet, while Cpt. Kara Thrace and Lee Adama organize resistance on board the Galactica and try to retake control of the ship. Zarek brings in Romo Lampkin to serve as Admiral Adama's defense counsel, against both Lampkin's and Adama's will. After a brief trial, Zarek, acting as judge, condemns Adama to death by firing squad. Zarek travels to Colonial One to attempt to solidify his position with the support of the Quorum of Twelve (absent Lee Adama). When they reject his coup and ask him to leave, he has two marines execute the entire group. Meanwhile, Kara and Lee rescue the high-profile prisoners taken in "The Oath" (Samuel Anders, Colonel Tigh, Sharon Agathon, as well as Helo, Hera and Caprica-Six), and with the help of Aaron Kelly rescue Admiral Adama from execution. Laura Roslin and her allies on the Cylon basestar, now under threat of attack from Gaeta and the Galactica, position the ship among the fleet to temporarily shield themselves. With Adama certain to be killed, the Cylons vote to jump away, but Roslin convinces them to stay with the fleet.
Adama and his allies, including some former rebels, march to retake the CIC. During a skirmish, Anders is shot in the neck, and Kara convinces Romo Lampkin to help her carry him to Dr. Cottle. In the CIC, Gaeta and Zarek are in the middle of a standoff with President Roslin. Zarek lies that Adama has already been killed, and Roslin vows to take vengeance. Gaeta orders the ship to jump away, but Tyrol has sabotaged the FTL drive, and Gaeta realizes the mutiny is failing. Adama and his men storm the CIC and the mutineers give up without a fight. After the CIC is reclaimed, Tyrol, who is still in the engine room, notices and inspects a heavily damaged section of wall. Long linear grooves appear to have been gouged into the steel. It is unclear what caused this damage.
Gaeta has a final conversation with Gaius Baltar before being executed. Gaeta and Zarek are executed for their actions by a firing squad, but seconds before, Gaeta realizes the phantom pains in his amputated leg have finally stopped.