Adam Stanheight (Leigh Whannell), a photographer, awakens in a water-filled bathtub in an industrial bathroom. Across the room from him is Lawrence Gordon (Cary Elwes), an oncologist. Both men are chained at the ankle to pipes, and a corpse is lying face-down in a pool of blood between them, holding a microcassette recorder and a revolver. They find tapes in their pockets, and Adam is able to retrieve the recorder. Adam's tape instructs him to escape, while Lawrence's tape instructs him to kill Adam before six o'clock, or Alison and Diana (Monica Potter and Makenzie Vega), his wife and daughter, will be killed and he will be left to die. Using a clue at the end of the message, Adam finds a bag in the toilet tank containing two hacksaws, which they use to try cutting through the chains. Adam breaks his, and throws it at the mirror in frustration. Lawrence realizes that the saws are actually meant for their feet. He tells Adam that they were captured by the Jigsaw Killer, who Lawrence is aware of because he was once a suspect.
Instead of using a dummy, Tobin Bell lay on the floor for the entire time of shooting and only got up while Wan was shooting Elwes and Whannell in the room.
Flashbacks show five months earlier, while Lawrence was talking to some students and an orderly named Zep Hindle (Michael Emerson) about a patient named John Kramer, who suffers from an inoperable frontal lobe tumor, Lawrence was approached by Detectives David Tapp (Danny Glover) and Steven Sing (Ken Leung), who found Lawrence's penlight at the scene of a Jigsaw "game". An alibi clears him, but he agrees to view the testimony of Amanda Young (Shawnee Smith), a heroin addict and the only known survivor of a game. Though Amanda is visibly traumatized by the experience, during which she killed a man to save herself, she genuinely believes that Jigsaw helped her. Other victims include Paul (Mike Butters), who had to get through a caged-in razor-wire maze, and Mark (Paul Gutrecht), who was nude and smeared with a flammable substance and had to obtain an antidote for the poison in his body from a safe by locating the combination on the room's walls with a candle, while having to walk across broken glass barefoot.
Meanwhile, Alison and Diana are being held captive in their home by a man watching Adam and Lawrence through a camera hidden behind the bathroom's two-way mirror. The house is simultaneously being watched by Tapp, who was discharged from the force. Flashbacks reveal that Tapp and Sing found Jigsaw's lair using the videotape from Amanda's game. They saved a man who was bound to a chair with drills set to pierce his neck, but Jigsaw fled after slashing Tapp's throat with a concealed blade, and Sing was killed by a shotgun booby trap while pursuing him. Tapp was then discharged for entering Jigsaw's lair without a warrant. In the bathroom, Adam and Lawrence follow a clue and find a box containing a lighter, two cigarettes, and a one-way cellphone. They attempt to use a cigarette to stage Adam's death, but this is foiled when Adam's ankle chain suddenly gives him an electric shock.
Adam then recalls returning home to develop photos and finding a puppet in his apartment. While searching for an intruder using camera flashes as light, he was attacked by a pig-masked figure. The abduction was similar to Lawrence's, who was in a parking garage when a pig-masked figure abducted him. Lawrence then receives a call from Alison, who tells him not to trust Adam. At Lawrence's prompting, Adam admits he was being paid to take photos of Lawrence, showing him photos from the bag that contained the hacksaws. This starts an argument, during which it is revealed that Lawrence was having an affair with one of his medical students (Alexandra Bokyun Chun), therefore revealing why Jigsaw chose Lawrence. It is also revealed that the man paying Adam was Tapp, who became obsessed with the Jigsaw case after Sing's death and began stalking Lawrence, convinced that he was Jigsaw. As Lawrence begins to realize how he took his family for granted, Adam points out a photo that wasn't taken by him, of a man staring out a window of Lawrence's house. Lawrence recognizes him as Zep, who is revealed to be the man holding Alison and Diana captive. The clock strikes six as he realizes this.
Alison, who managed to untie herself, attacks Zep as he holds the phone to her ear, and they fight for the gun. The struggle gains Tapp's attention and he arrives in time to save Alison and Diana. He then chases Zep, who flees to the sewers, and catches up only to be shot after a brief struggle. Lawrence, who only heard gunshots and screaming, is shocked and loses reach of the phone. Out of sheer desperation, he saws his foot off and shoots Adam with the corpse's revolver. Zep enters the bathroom intent on killing Lawrence, but is blindsided and beaten to death with a toilet tank cover by Adam, who suffered only a flesh wound. As Lawrence crawls away to find help, Adam searches Zep's body for a key and finds another recorder, which reveals that Zep was another victim: he was instructed to hold Lawrence's family captive in order to obtain an antidote for a slow-acting poison in his body. As the tape ends, the unidentified corpse rises to its feet and reveals itself as John Kramer, the real Jigsaw Killer. He tells Adam that the key to the shackle is in the bathtub, which was drained when he first awoke. Adam attempts to shoot John, who shocks Adam and causes him to lose reach of Zep's gun. John then turns off the lights and seals the bathroom door, leaving Adam to die.
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