In the previous episode, the fleet's leadership announced its plan to upgrade the fleet's jump drives using Cylon technology to triple its reach in searching for a final home. Felix Gaeta, betrayed by Cylons on several occasions, vehemently opposes the plan. Finally, he makes a pact with Tom Zarek, as of then not fully disclosed, to, in his words, rectify things that have gone wrong. The episode has a survivor count of 39,643
Gaeta helps Zarek to jailbreak from the Galactica onto Colonial One. There, Zarek talks Lee Adama into leaving Colonial One and returning to Galactica, to request from Admiral Adama the reason for letting Zarek go. In the meantime, Gaeta organizes a full scale mutiny onboard Galactica, with the civilians arming themselves using weapons from Galactica's weapons lockers. Kara Thrace notices the uprising, and tries to get confirmation on what is happening, but is denied the information, being repelled on the grounds of her status being unknown after the events of Sometimes a Great Notion. Officers of the fleet who have mutinied, among them prominent people like Racetrack, Narcho and Skulls, take Lee Adama hostage upon arrival on the Galactica. He is promptly rescued by Thrace. They flee together, and decide to try to remedy the situation to whatever extent is in their reach.
Rebel crew imprison Samuel Anders, as well as Karl Agathon and his wife Sharon Agathon, and their child, Hera Agathon, together with Caprica Six in a brig cell. In the CIC, Admiral Adama and Saul Tigh are taken hostage and sent to the brig as well. Adama and Tigh manage to overwhelm their captors and break free. Lee Adama and Capt. Thrace help President Laura Roslin (who has decided to take an active role in government again) meet with Gaius Baltar in order for her to use Baltar's wireless transmitter to address the fleet and bring the people back into order; afterwards they join up by coincidence with Admiral Adama and Tigh. Together they make their way to Storage Bay Two, from where Galen Tyrol has promised to take the Admiral and the President into safety onto the rebel Cylon basestar.
Zarek keeps control of the situation from Colonial One. His intentions were, as it turns out, to have Admiral Adama killed, and he is dissatisfied that this didn't happen.
Alone in the storage bay, Baltar and Roslin come back closer together. They realize that they finally have more in common than it seemed all along. Roslin finally makes it off the Galactica with Tyrol's help; Gaeta however orders their Raptor to be destroyed. Saul Tigh and Admiral Adama defend the storage bay from where the Raptor took off, only to be attacked by rebel marines. Both Tigh and Adama's as well as the Raptor's fate remain uncertain at the end of the episode.