At the research facility, we see Jon, Wally and Janey walking down the hall to the cafeteria, when Jon realizes he forgot his watch. He goes back for it, finding it in the intrinsic field generator chamber, where the door closes behind him. The countdown begins, and he realizes he can't get out. Wally and Janey come back to find him, and Wally tells him there's nothing he can do. Lightning is beginning to play across the walls of the box. Janey starts to cry, tells Jon that she can't watch, then runs off to find another boyfriend.
Some of what follows has been seen in the first Watchmen trailer. Lightning crackles up Jon's arm hair, and he looks at his watch, which starts to slow down, or perhaps our perception of time does. Manhattan flashes back to the first time he met Janey, when she bought him a beer, the first time a woman had done that for him. At the time of the accident, Wally backs away from the chamber. We go back to Jon's teen years this time, when he was being taught how to take apart and put back together the minute gears of a pocket watch. His father stands over him and helps him. In the chamber, adult Jon convulses once and is then torn apart by the intrinsic field. Even his skeleton is vaporized. We see much more viscera than the trailer allowed.
A "token funeral" is held, since there is no body. But later, a glowing circulatory system is seen near the facility's outer fence. It's like a giant jellyfish-man; the MP on duty looks pretty freaked-out. Later, a partially muscled skeleton, also glowing, is seen in a hallway, and it slams against a wall before dissipating into an expanding energy wave that knocks the janitor off his feet. (This shot and part of the next are seen in the trailer.) Next, we see Wally and Janey eating lunch in the cafeteria, looking pretty depressed, when the whole place starts to shake. The blue, glowing body of Dr. Manhattan materializes in mid-air, as small metal objects like spoons and forks orbit around him. We see a close-up of Janey's face, as a spoon drifts by, and she says, "Jon?" Cut to a newscaster reporting that "The Superman has been discovered, and he's American."
We see Dr. Manhattan wearing a suit at a press conference, as he voiceovers an explanation of his superhero name. It's meant to be an ominous reference to the Manhattan Project, which developed the atomic bomb. Later, in his first superhero outfit, which looks like a wrestling singlet, he marks his forehead with a drawing of a hydrogen atom. At a test of his abilities in the New Mexico desert, Manhattan points at a tank, disassembles it into its component parts, then mashes them back together into a giant ball and drops it. We see him meeting with Nixon, who asks him to go to Vietnam, and he goes, ending the war within a week. We see Viet Cong troops kneeling in front of him as if in worship, as he voice-overs that many of the enemy generals asked to surrender to him personally. (He was still wearing pants in those days. Otherwise, they might have been happy waving to him from a distance.)