The episode begins directly after the cliffhanger of the previous episode, where Kara Thrace holds Laura Roslin at gunpoint to stop her from going to what she thinks is the wrong way to Earth. Meanwhile, some of the Humanoid Cylon models wish to lobotomize the Raiders to make them destroy the fleet, regardless if the final five are among the fleet. However, the other Cylon models, particularly Natalie (a Six model) wish to stop them by any means necessary. The survivor count shown in the title sequence is 39,676
Kara Thrace holds President Laura Roslin at gunpoint and reminds her that she once followed orders from Roslin to find Earth. Now that Starbuck thinks she knows where Earth is, Roslin rejects it. Feeling betrayed, Starbuck tells Roslin to take the gun and shoot her if she can't trust her. Roslin does pick up the gun and just as security arrives she fires and misses. Starbuck is quickly taken to the brig but urges everyone to change course. She fears that she will lose her directions to Earth forever if they make one more jump. Admiral Adama confronts her, telling her she has lost all hope of anyone helping her. After Starbuck accuses Adama of ignoring her on purpose, Adama furiously slams her to the deck then leaves in disgust. Later, the fleet makes another jump, and Starbuck loses her direction of Earth.
The Cylon models prepare to lobotomize the Raiders to forget about the Final Five as their identities are forbidden by their programming. They vote but it ends in a draw (Number One, Number Four and Number Five votes for, and Number Two, Number Six and Number Eight voting against). Boomer is the only Eight model to vote for the lobotomizing. To prevent this from happening, one of the Six models (known as Natalie) removes the higher brain inhibitors from the Centurions which gives them free will. They proceed to kill all of the One, Four and Five models in the room.
Lee Adama leaves Galactica to start his new political career, but not before telling Starbuck that he believes her. The four Cylons (Colonel Tigh, Tory Foster, Samuel Anders, and Galen Tyrol) meet in secret to discuss who they think is the fifth Cylon. Since they believe Gaius Baltar may know, Tory visits him. At first, Baltar believes she is spying on him. After having a vision of his virtual self, he and Tory talk, and later sleep together. Afterward Tory says that she could be a Cylon, but Baltar tells her not to be afraid and that he has learned from his time among them that Cylons have feelings. He says that humans may have created the Cylons, but it was the one true God that gave them souls. Adama and Roslin discuss what to do with Starbuck. Though Roslin has objections, Adama eventually decides to let Starbuck go. In the end, she is taken to a hangar, where to her surprise, she is given a ship, the Demetrius and a team including Helo, Athena, Anders and Gaeta to find Earth