The command center has been seized and Admiral Adama sends President Roslin to the Cylon Baseship; right after the President leaves on a Raptor, Admiral Adama and Colonel Tigh are captured. Lt. Gaeta order his fighters to shoot down the Raptor with the President on board. Using communications, she is able to stop it from happening. This is all in the opening sequence. For a large part of the episode there is a lot of deception from Tom Zarek and Lt. Gaeta. In one scene Zarek has the whole quorum shot and killed for not agreeing with him. With the help of Starbuck and Lee the Cylons being held are rescued. When Zarek finds this out he tells Admiral Adama that Colonel Tigh was shot trying to escape. Adama is sentenced to die in a bogus trial with Zarek as the Judge. As Admiral Adama is about to be executed, Lee Adama, Colonel and their team stop it and gain control of the situation.
During all this time the Chief has been crawling through air vents and passageways to get to the FTL drive and shut it down. He cannot logon with his account because it has been disabled. He proceeds to pull out the FTL drive just seconds before it is encaged.
After Admiral Adama is rescued, they all take control of the command center and Galactica. The fleet is back in control of the President and Adama.
The final scene is the business of executing Lt. Gaeta and Tom Zarek.