As Rorschach, whose real name is revealed to be Walter Kovacs, gets acclimated to life inside a federal prison, the details of his childhood and origins as a vigilante are recounted by the unmasked crimefighter during sessions with a prison psychologist.

During his self-exile on Mars, Dr. Manhattan recalls his youth as Jon Osterman, son of a watchmaker who forced him into a career in nuclear physics. But a terrible accident in an atomic lab turns Osterman into a radioactive “super being” causing him to sacrifice his relationship with his first love.

Midnight, November 2, 1985. Most of New York City has been devastated by the psychic trauma caused by the instant death of Ozymandias’ teleported “alien.” Dr. Manhattan and heavily distraught Laurie tour the devastation. After they have seen enough, the two teleport away to the South Pole, to follow a trail of tachyon particles that Dr. Manhattan senses will lead to the source of the disturbance.

This chapter is set against The Comedian’s funeral where Silk Spectre recalls her horrific assault at the hands of The Comedian and while Nite Owl and Dr. Manhattan recount their own experiences that reveal The Comedian to have been a larger-than-life enigma: a hero and a villain in one costume.

As Rorschach and Nite-Owl approach Veidt’s Antarctic retreat, they discuss whether or not their old crime fighting partner would actually want the world destroyed.

A murder takes place in New York City. "The Comedian," a former costumed crime fighter, was thrown out the window of a skyscraper. This event triggers an investigation that rounds up many of The Comedian's former superhero allies, who are now banned from carrying out any acts of "justice."

Laurie and Dan start putting together pieces of a conspiracy that leads them to the decision to go break Rorschach out of prison. When they all return to Dan's apartment, Dr. Manhattan return from his self-exile on Mars and wisks Laurie away so they can discuss the situation.

Dr. Manhattan takes Laurie to Mars, and embarks on a journey back through time, reliving the events of Laurie’s past in order to find clues about the nature of humanity and how he might be able to affect the turmoil that is choking the world. After many revalations, Dr. Manhattan decides what he must do.

Rorschach continues his investigation into the murder of The Comedian as another former costumed hero, Ozymandias, is attacked and almost killed. But when Rorschach follows up a lead at a retired super villian’s apartment, he is caught by the police and has his face revealed for the first time.

As Russian tanks mass along the East German border, President Nixon and Vice President Ford head deep inside a government emergency bunker. Before continuing their investigation, Rorschach and Nite-Owl head back to Rorschach’s apartment to pick up his spare costume and journal.

As the world braces for what could be a doomsday scenario between the U.S. and Russia, Laurie leaves Dr. Manhattan and goes to Dan for consoling. Meanwhile, the media puts Dr. Manhattan under scrutiny, linking him to a rash of cancer deaths, and forcing him to escape to the planet Mars.

A depressed Dan gives Laurie a tour of his basement and all of his old crime fighting equipment. Later, Dan tires to make love to Laurie but just can’t get himself going. After she discovers Dan sulking, Laurie convinces Dan to suit up in his old costume and go for a ride in the Owl Ship.