On Kobol, the crew of Raptor One get out of the quickly burning Raptor. As Baltar is about to get out, flames spring up in front of him. Believing he's going to die, he sees a vision of Six, who asks him to take her hand. She pulls him out of the burning Raptor...and Baltar wakes up in the real world, being pulled out of the Raptor by Crashdown. Just as he and Crashdown get out of Raptor One, it explodes. Baltar wanders off as the rest of the crew help each other, and collapses in exhaustion.
On Caprica, Helo and Boomer are sitting out side the Museum of the Colonies in Delphi. Boomer explains that the Museum is the home of the Arrow of Apollo. Boomer tells him they should go in at night.
On Galactica, Tigh and Adama are wondering why Starbuck would disobey orders, and call the President. Roslin admits she had Starbuck take the Cylon Raider back to Caprica. When Adama terminates her presidency, she stands firm in her decision and tells Adama he'll have to come over to Colonial One and get her himself. Adama orders Tigh and Apollo to take a team or Marines to bring in Roslin, while at the same time Adama formulates a plan to use a Raptor and one of the Cylon transponders to get a nuke inside the Cylon base ship orbiting Kobol. He gets Boomer to pilot the Raptor.
Starbuck's Cylon Raider reaches Caprica, and she heads for the Museum. Outside the Museum, Boomer tells Helo that their relationship was important in bringing them closer to God. She also tells him she's pregnant.
The Marines reach Colonial One and begin to board it. Boomer and a new pilot, Racetrack, jump to Kobol, after being given a "good luck" by Adama. Onboard Colonial One, Roslin urges her men to go to the cargo hold with the civilians. All of them decide to stay, as Billy receives confirmation that the Marines are indeed coming, with sounds of someone cutting through then hull.
On Caprica, Starbuck lands near the Delphi Museum. After injecting herself with anti-radiation medicine, she proceeds into the Museum.
Boomer and Racetrack reach Kobol, and the transponder manages to fool the Cylons. However, when she attempts to fire the nuke, it becomes jammed. Boomer decides there's only one alternative : go into the base ship itself and detonate the nuke. After some arguing with Racetrack, Boomer takes the Raptor into the base ship.
On Kobol, Crashdown gets into an "argument" with Chief Tyrol about whether they should hide from the Cylons or get to high ground. Baltar wakes up and sees Number Six standing over him. She asks if he wants to find out why he's "been chosen to survive and serve God's purpose", and that now's the time to find out why. She takes his hand and leads him towards some ruins.
On Colonial One, Roslin's men get out guns and prepare for a fight. After a short prayer from Elosha, they hear sounds of the Marines coming closer.
On Caprica, Starbucks finds the Arrow of Apollo. Just as she picks it up, a Number Six walks up behind her. She and Starbuck begin to fight.
Boomer's Raptor gets inside the base star, and Boomer prepares to release the nuke. As the Raptor lands and the nuke it released, several naked women walk up towards Boomer. As the shadows covering them begin to fade, Boomer finds herself looking at multiple copies of…herself.
Starbuck and Number Six continue their fight, and it appears as if Number Six is going to win. Behind her, Helo and Boomer walk up, Helo getting ready to fire. Suddenly Starbuck knocks Number Six, along with the Arrow, into a hole in the floor. They both land heavily, and Helo runs to investigate.
On Colonial One, the Marines break into Roslin's main compartment, and both sides aim their guns at each other. Apollo has a change of heart, deciding Roslin shouldn't be arrested just because she made a bad decision. He aims his gun at Tigh's head. After a few seconds, Roslin askes Apollo to drop his gun, deciding to go quietly. Apollo and Roslin are arrested.
Inside the base ship, the copies of Boomer tell her she can't run from destiny, and that it'll catch up with her no matter what she does. After learning the horrible truth, that she is in fact a Cylon, Boomer bolts back to the Raptor, and she and Racetrack escape, just as the base ship explodes.
On Caprica, Helo and Starbuck reunite, but the happy reunion is cut short when Starbuck sees Boomer nearby, and works out Boomer's a Cylon. Once Helo tells Starbuck Boomer's pregnant, it's too much and Starbuck collapses.
On Kobol, Number Six leads Baltar into some ruins, which then become the Kobol Opera House. Baltar and Number Six walk up to the stage of the Opera House and stand over a glowing white cradle. Number Six comments, "Isn't she beautiful, Gaius?" and the two of them kiss.
Onboard Galactica, Adama puts Roslin in the brig. He walks onto the C.I.C. and congratulates Boomer and Racetrack for destroying the base ship. However, just as he thanks Boomer, she raises her hand to shake his…and reveals a gun. She shoots Adama twice at close range. Tigh and Apollo try to stop the bleeding, and Boomer is knocked to the ground by guards. Apollo and Tigh both put their hands on Adama's wounds, screaming for a doctor. Dualla holds Adama's hand, and Boomer just watches in shock at what she's done.