Seth Baxter (Joris Jarsky), a convicted murderer, awakens chained to a table beneath a pendulum blade. In order to release himself, he must crush his hands by putting them into two presses and pushing the buttons inside. He does as the video tells him, but the pendulum still swings down and violently cuts him in half. Just before he dies, he sees an eye watching him through a hole in the wall.
In a scene from the end of Saw IV, Agent Peter Strahm (Scott Patterson) finds and kills Jeff Denlon (Angus Macfadyen) in self-defense. After being sealed in the sickroom with the corpses, he escapes through a hidden passage, where he is captured by a figure wearing a pig mask. He awakens with his head trapped in a glass box slowly being filled with water; he performs a tracheotomy using a pen, which keeps him breathing. Outside the meatpacking plant, Detective Mark Hoffman (Costas Mandylor) returns Corbett Denlon (Niamh Wilson), Jeff's daughter, to the police. He claims they are the only two survivors, only to be shocked to see Strahm carried out alive as well.
Jill Tuck (Betsy Russell) obtains a box and videotape, left for her by John Kramer (Tobin Bell). The tape informs her that the items in the box are of "grave importance"; she opens the box using a key around her neck and looks inside, then leaves without disclosing its contents. Meanwhile, a memorial service is held for Officers Tapp, Sing, Kerry, Matthews and Rigg; during the memorial, Hoffman is promoted to detective lieutenant by the chief of police. While taking Strahm's mobile phone, he is informed that Lindsey Perez (Athena Karkanis), Strahm's partner, died from her wounds. He confronts Strahm at the hospital, who informs him that Perez's last words were "Detective Hoffman". Strahm is taken off of duty by his boss, Dan Erickson (Mark Rolston), and begins researching past Jigsaw victims, now obsessed with piecing together Hoffman's involvement. He learns through his research that Hoffman killed Seth Baxter with the pendulum trap after Seth killed his sister, and that John used his information of this murder to blackmail Hoffman into working with him. The two worked together to set up most of John's tests, most notably the razor-wire maze and the nerve gas house. Additionally, Hoffman planted the penlight that framed Dr. Lawrence Gordon and provided the files for the victims of the gas house. Near the end of his quest, he realizes that everyone was meant to die in the meatpacking plant except for Hoffman, who was to escape as the hero.
While Strahm pieces together Hoffman's involvement with Jigsaw, five more victims awaken in a trap taking place in a sewer. Collars are locked around their necks that connect them to razor blades mounted on the wall behind them; the keys to their collars are in glass boxes on the other end of the room, but moving for them will set off a one-minute timer. All but Ashley (Laura Gordon) retrieve their keys, and she is decapitated when her collar retracts. In the next room, keys must be found in jars hanging from the ceiling in order to unlock three chambers that will provide shelter from an explosion. Charles (Carlo Rota) attacks Mallick (Greg Bryk) and takes his key, but is struck by Luba Gibbs (Meagan Good) and is killed when the bombs explode. In the third room, five cables must be connected to a full bathtub to unlock five locks on the door, though none are long enough to reach. Luba attacks Mallick to use his body to close the circuits, but Brit (Julie Benz) foils this plan by stabbing her in the neck; they use Luba's body to close the circuits. In the final room, the door must be opened by filling a beaker, positioned in a machine fitted with circular saws, with ten pints of blood. They notice that there are five armholes and realize that all five victims were to work together to survive in every game. They also realize that all five of them were connected to a building fire that killed eight people. With no other choices, they begin sawing their arms to provide the ten pints.
Meanwhile, Hoffman plants Strahm's phone and Erickson's FBI personnel file at the exit from this room. Erickson arrives here just as Brit and Mallick get the door open. Mallick passes out from blood loss while Brit crawls out and is found by Erickson, who finds the phone and file as well. He calls for medical assistance for the two victims, then places an all-points bulletin out for Strahm's arrest. Simultaneously, Strahm follows Hoffman to the renovated nerve gas house and makes his way to a small underground room, which contains a clear box filled with broken pieces of glass. A microcassette left by Hoffman states that Strahm must trust him and enter the box, but Strahm stops the tape short and ambushes Hoffman when he arrives, ultimately sealing Hoffman in the box and subsequently causing the room to seal itself. Hoffman indicates the tape, which continues by telling Strahm that by choosing not to comply, he will "simply vanish" and Hoffman's legacy will become his own. The glass box is lowered safely into the floor, while the walls close in on Strahm, who attempts to escape through the ceiling grid, but he is eventually crushed to death.