Kara breaks into Adama’s quarters and pulls a gun at the President. She tells Roslin that she resents her, she is angry and disgusted at her before handing her gun to her. She tells her to shoot if she truly thinks she is a Cylon as Tigh, Adama and soldiers start rushing into the quarters.
A shot is fired and Roslin winds up hitting a picture of her and Adama instead of Kara. The troops rush in and they restrain Kara, who keeps screaming that she knows the way to Earth and they are making a mistake. At the brig, Adama confronts Starbuck over her earlier actions but Kara taunts him by claiming he is spineless and the President’s wet nurse. The admiral throws her down the floor and leaves but not before Kara screams that they are heading the wrong way.
Meanwhile, the Number Six, Eight and Two models observe a hybrid giving random rants about the Final Five and random predictions on their nature. After hearing the hybrid, the three models bring up the Final Five to the rest of the humanoid models. Cavil calls the talk of the Final Five against their nature and is alarmed at the independence the raiders started asserting after it is suspected of finding the Final Five among the Colonial fleet.
The 6 Cylon models debate amongst themselves about the raiders withdrawal from the last episode and of the final 5. Cavil demands Number Six to stop talking about the Final Five and suggests the idea to lobotomise all the Cylon Raiders who have become more assertive after one of them scanned Anders in the battle. The final vote comes down to a deadlock with 6, 8 and 2 voting against the reprogramming the raiders while the 1, 5 and 4 support it.
The Number Six known as Natalie points out they are at a deadlock but Cavil (Number One) brings in Boomer who has decided to vote with them. He points out that Natalie was right that some things are changing among them like a Number Eight voting differently from the rest of her model. This is considered absurd by Natalie’s faction as all models are expected to vote as one bloc. As a result of the changed vote, the lobotomy begins for the raiders and it is depicted in an extremely graphic fashion showing the Number Fours gutting the Raiders’ organic brains.
Later, Number Six returns to confront the other Cylons who supported to lobotomy. It turns out the opposing bloc retaliates by having Number Eight remove all inhibitors from their Centurion counterparts, which upgrades their AI to allow for basic reasoning. After learning about what the Number Ones, Fours and Fives did to the raiders, the Centurions kill them with Natalie watching in horror.
Back on the Galactica, the Final Four are still debating who the fifth cylon is until Galen suggests Baltar as a suspect. With this in mind Tigh asks Tory to meet and seduce Baltar to get confirmation since there are rumours that Baltar is preaching monotheism and cured a sick child. Tory later goes to the mess hall to meet with Baltar, who is tempted by her, but initially distrusts her since she is Roslin’s aide. However, Virtual Baltar talks him into it and Baltar finds it strange since he usually sees a Virtual Six.
Later Tory and Baltar have sex and she seems to be convinced of his views of a “One True God” but does not think he is a Cylon.
Lee Adama decides to leave the military for a career in politics. His comrades throw him a going away party and later a public service for his contributions to the Galactica. Prior to leaving Lee visits Kara at the brig and they share a passionate kiss with Lee telling her he believes her.
Admiral Adama visits Roslin shortly after Lee’s informal party to discuss Kara. The President tells her that they can’t trust someone who simply appeared as a miracle while Bill tells her off for being someone who is afraid to die alone and to die as a failure. Roslin informs Bill that she is dying, implying the cancer is back, she is seen loosing chunks of hair when she casually brushes her hair after the discussion.
Adama eventually releases Kara from the brig and sends her and Karl to crew the Demetrius who will secretly find the path to Earth while officially acting as a scout ship for the fleet. With this in mind, Kara thanks Adama and the episode ends.
Next week’s episode shows previews of Natalie sending the resurrected Cavil, Fours and Fives off the Cylon basestar, Cally learning of Galen’s Cylon nature, Tigh deciding how to keep their secrets and Tory killing Cally with the airlock while holding her baby.