The film begins with Detective Eric Matthews (Donnie Wahlberg) chained by his ankle in the same dilapidated bathroom in which he was imprisoned at the end of Saw II. He quickly discovers a hacksaw next to him, but attempts to cut the chain prove futile. After seeing Dr. Gordon's severed foot, he realizes he must saw his own foot off to live. He decides instead to crush the bones in his foot, with the toilet's tank cover, so that he can slip it out of the ankle cuff.
Elsewhere, Rigg (Lyriq Bent) leads a SWAT team inside an abandoned room where they find the remains of a body. A forensic expert informs Detective Kerry (Dina Meyer), the "Jigsaw expert", that the corpse is not Detective Matthews, as she initially feared, but a man named Troy.
Through a flashback, we see Troy awake in the abandoned room; chains attatched to the walls are hooked into his skin. One particular chain latched to the floor is wrapped around his mandible. A television screen turns on, and Jigsaw's puppet, Billy, is shown. Billy speaks to Troy about how, despite the many advantages he was given at birth, he's been in and out of prisons, seemingly finding more comfort in chains than being free. To live, he must break free of numerous chains (with terminal links affixed through various body parts). The television screen turns off, and he notices a bomb planted nearby, with 1 minute and 30 seconds ticking down. Troy failed to free himself in time. Kerry notes this particular trap does not fit Jigsaw's usual pattern, as Jigsaw's "games" give their victims a chance to escape if they were successful. The door to the room was welded shut, and would not have allowed Troy to escape regardless.
Kerry takes the recovered tape home to review, but is kidnapped herself when she attempts to investigate a camera source that is videotaping her live inside her own room. Kerry wakes up hanging from a ceiling in a metal contraption when a video starts on a nearby TV screen. We once again see the puppet. It then proceeds to tell her that she has spent all of her life living amongst the dead, and identifies with them more than she does the living. He reveals that the device she is wearing is hooked into her ribcage. She has one minute to retrieve the key from the jar of acid before it fully dissolves. She manages to get a hold of the key and unlock her chest piece. However, this does nothing, as the contraption is still lodged in her chest. A cloaked figure walks into the room (Amanda), and Kerry immediately realizes who it is. She finally gives up and prepares to die. She lifts herself up from her chains as the device rips out her ribcage, killing her instantly.
Elsewhere, Dr. Lynn Denlon (Bahar Soomekh) finishes her shift at the hospital and prepares to leave, but finds herself trapped in the locker room. Amanda kidnaps her and brings her to Jigsaw's new lair. Lynn wakes up to find herself tied to a wheelchair. She is wheeled to Jigsaw, John Kramer, who is resting in a makeshift hospital room. After asking Lynn how long he has to live, Jigsaw says that he ???wants to play a game.??ť Amanda equips Lynn with a bulky collar surrounded by shotgun shells. The collar contraption is linked with Jigsaw's heart rate monitor. If Jigsaw flat lines, or if she strays too far from him, the shells will fire, killing her. It is explained that another man is also being tested, and if he completes his tests before Jigsaw dies, she is free to go.
This man being tested is Jeff Reinhart (Angus Macfadyen), who wakes in a wooden crate suspended by a forklift. He finds a tape recorder which tells him that he is still consumed with hatred for those involved in his son Dylan's (Stefan Georgiou) death. The tape also tells him that he must suffer and forgive in order to pass his tests and escape. His final test will be confronting the man responsible for the loss of his child. However, if he takes longer than two hours, the doors will lock and seal him inside forever. Jeff quickly breaks free and falls to the ground. In a flashback sequence, his rage is explored. Moments later, Jeff finds an open box containing a piece of paper with the words "Open the door, Jeff." typed on it. Along with it is a piece of photograph (showing him) and a key.
Lynn explains to Amanda that Jigsaw has a brain herniation and his only hope is to get care from a hospital, but Amanda won't permit leaving. After Lynn and Amanda stabilize Jigsaw, from a sudden seizure, Amanda asks for the tools needed to fix the hernia. Lynn tells her she'll need anesthesia and a power drill.
Nearby, Jeff enters a room with "FACE YOUR FEARS" painted on the door. The room is a freezer, and in the middle is where Danica Scott (Debra McCabe) is shown hanging by her arms, where two vertical poles spray her naked body with cold water. In her tape, it is revealed that Danica was the only witness at the scene of the car accident. Jigsaw gives Jeff the choice to save her or let her freeze to death. In this trap, behind freezing cold pipes, there is a key that Jeff can reach to save her. Jeff hesitates to do so, claiming that she "did nothing" to help his son. As he deals with his dilemma, Danica screams from the excruciating pain. He eventually retrieves the key, but she freezes to death before he can rescue her. Jeff finds another box outside the room. Written on this paper is "One bullet will end it all." Inside, along with a single bullet, is another piece of the original photograph, this time showing his son.
In the hallway, he finds Billy lying motionless next to his tricycle. They are positioned in a manner that resembles his son's accident. Billy turns his head to Jeff and begins laughing in mockery. Upon entering the next room marked "TIME TO LET GO," Jeff hears the voice of a man screaming for help. He climbs up a staircase to see a man pinned to the bottom of a silo by a metal collar around his neck. As he screams for help, Jeff plays the tape recorder hanging from the ceiling. Jigsaw's voice tells him that when the judge presiding over his son's murder trial sentenced the murderer so lightly, his soul never recovered. He now has the power to sentence the man's soul straight to hell, or he can choose to forgive. The man inside the silo is that very same judge. In order to get the next key, Jeff must activate an incinerator containing his son's possessions, which he had clung to for so long. As the tape ends, a series of large, interlocking saws connected to the silo begin to whirl and buzz, and a conveyor-like bar turns on sending out dead, maggot-filled pigs. The pig is dropped onto the saw blades, and the liquefied results expelled into the silo, splashing over Judge Halden. After expressing his anger to the judge, he reluctantly hits the button and watches his son's possessions burn. Jeff is able to retrieve the key and climbs into the silo, narrowly freeing the judge before he was completely submerged.
Lynn prepares to operate on Jigsaw under local anesthetic. She uses a power drill and then a bone saw to cut open a hole in his skull to relieve the pressure the tumor is causing. John's heart rate begins to decrease and he starts having flashbacks in which he is seen with his former lover, Jill. He soon stabilizes and Amanda watches as he holds Lynn's arm and says he loves her, still momentarily stuck in his hallucination. Jealous, Amanda leaves. Stricken with grief, she cuts herself on the thigh, a new addition to numerous scars assumed to be from the same practice before. She then has a flashback of her own, where we see Jigsaw preparing for the Reverse Bear Trap from the first film. It is also revealed that he confronted her at her apartment after she escaped and asked her to be his apprentice, and her first task was to kidnap Dr. Lawrence Gordon and Adam Faulnker, who were the test subjects of the infamous Bathroom Trap.
After this, Amanda enters and hugs John, only to be scolded by Lynn for touching him. Amanda confronts Lynn, about to brandish a gun, but John interferes and tells Amanda to leave.
Jeff and Judge Halden find a box with another piece of the photograph, this time with Jeff's daughter depicted, along with a ammo clip for a pistol and a card reading "One step closer to revenge." They then enter a room with "HERE'S YOUR CHANCE" painted on the door. 'The Rack' is in the center of the room, where the next victim is bound. As Jeff plays his tape, Jigsaw's voice reveals that the man is Timothy Young, a 27 years old victim who killed Jeff's son. He implores Jeff to realize that Timothy's guilt over Dylan's death equals his grief, and to see him as a human being. Tim's head, arms, and legs are attached to the metal machine in the shape of a cross, each end able to twist 360 degrees. The key is connected to a shotgun, requiring Jeff to take a bullet to save the man who killed his son. Jeff is crazed and hesitant at first, briefly making insight to the fact that he had wished to kill Tim for 3 years, and whether this really does make him a murderer, but he pushes his demons aside and tries to get the key off the chain. He realizes that the key can be removed without pulling the string, and when he removes the key the string triggers the shotgun. It narrowly misses him and instead kills Judge Halden. Tim screams of pain can be heard during the ordeal, the rack twisting his arms and legs and snapping his bones. Jeff frantically searches for the place to put the key, but runs out of time as the rack twists Tim's head 360 degrees, snapping his neck as Jeff watches.
Meanwhile, in the makeshift medical room, Jigsaw has a brief conversation with Lynn about her family and how she abandoned them. During the conversation, he reveals that he despises murderers, and also quotes the film's tagline, "Suffering? You haven't seen anything yet." Amanda reveals that Jeff passed the third test. Jigsaw tells Amanda to release Lynn, but she refuses, pointing her gun at Lynn. He attempts to calm her, claiming she would not be following the rules, but Amanda refuses to listen. Amanda lashes out at her mentor, claiming that no one learns anything from Jigsaw's games, citing Eric Matthews who she believed was the same person after his game that he was when he arrested her. Yet another flashback commences, where we discover that Eric Matthews managed to escape the bathroom and followed Amanda down the hall, where he confronted her. Hobbling along on his one good foot, he assaults her and repeatedly smashes her face into the wall, screaming "Where's my son?!" each time. However, she refuses to divulge this information, and instead takes advantage of his injury by kicking his broken foot. As we return to the present, Jigsaw continues to condemn his apprentice and it becomes apparent that Amanda never allowed any of the victims to actually leave the ???games??ť alive.
Jeff discovers a gun and inserts the magazine he found previously, before continuing down the corridors toward the exit. Jeff arrives in the makeshift hospital room, and as Lynn goes to embrace him Amanda shoots her in the back. Lynn collapses in Jeff's arms. Jeff immediately raises his gun and shoots Amanda in the neck. Jigsaw stares at her and reveals his true plan all along: Amanda was the one being tested. Lynn and Jeff were actually married, and he was the one who set up the boxes in the corridors for Jeff's tests. In his desperation to make her his true apprentice, after all the injustices she had committed with her murders, gave her one last chance. He also claims that all the "games" that Amanda had set up were impossible to survive, referring to Troy's welded room and Kerry's torso device. By disobeying the rules and shooting Lynn, she had failed and she died.
Jigsaw tells Jeff that Lynn is dying. If he cooperates, he can call an ambulance to arrive in four minutes. Jigsaw proposes one final test. On a nearby table, there are various tools about that Jeff can use to exact his revenge on Jigsaw, or he can forgive him for the pain he's caused Jeff and Lynn. "Live or Die," Jigsaw says, "make our choice." Jeff claims he forgives him, but then brandishes a circular power saw. Lynn desperately tries to tell Jeff to stop, but she can hardly speak. Jeff slices Jigsaw's throat open, once again proclaimes "I forgive you."
Jigsaw begins to flat line and reveals a tape recorder in his right hand, playing it. The tape reveals that Jigsaw himself was the final test. For as he said earlier, Jigsaw was the man responsible for the loss of Jeff's child: his daughter. Only he knows where she is, and she is running out of air. By killing him, Jeff has failed the final test, and learned nothing in his ordeal, or the location of his daughter. Lynn's collar light changes from green to red. The doors of the warehouse all latch shut. When Jigsaw's heart monitor flatlines, Lynn is killed when her collar fires, her head literally exploding against the wall behind her. Scenes from all three Saw movies flash by the screen as Jigsaw bleeds to death and dies, and Jeff screams in horror, trapped inside the warehouse...
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