The film is positioned as an interquel, taking place between the events of Saw I and Saw II. It focuses entirely on John Kramer / Jigsaw (Tobin Bell) during a period when he is desperately seeking a cure for his terminal cancer, long before his identity as the Jigsaw killer becomes widely known.

John, accompanied by his loyal apprentice Amanda Young, travels to Mexico City. He has heard rumors of an experimental and highly secretive medical procedure run by a group claiming to offer miracle cures for stage four cancer a last, desperate hope for John.

The supposed medical team is led by Cecilia Reyes, a charismatic but ruthless swindler. John undergoes a harrowing, expensive, and fake surgery, believing he has been cured. He later discovers, upon returning home, that the entire operation was a massive, cruel scam designed to exploit terminally ill patients, leaving him with no cure and no money.

Fueled by righteous fury and a renewed conviction in his philosophy that those who do not appreciate life deserve to be tested John decides to teach the scammers a lesson. He views their crime as unforgivable because they preyed on hope.

John and Amanda begin meticulously tracking down Cecilia and her core team of accomplices, including the manipulative Dr. Parker and the deceptive taxi driver Mateus, who were all complicit in the sham procedure. They kidnap the entire crew and transport them to a large, abandoned warehouse in Mexico City, which serves as the site for their new, intricate game.

The middle act consists of the victims navigating a series of John's most elaborate and cruel traps yet, all thematically tied to the specific ways they defrauded the sick. For example, one victim must cut out a portion of their own brain tissue to measure their "worth," while another must break every bone in their hands to escape a trap designed around the concept of "false healing."

A key twist occurs when Cecilia manages to gain the upper hand, briefly escaping and turning the tables on Amanda. She manages to capture and restrain both Amanda and, critically, John Kramer himself. Cecilia, seeking revenge, attempts to subject John to one of his own traps.

The climax reveals John’s master plan was two steps ahead. The trap Cecilia used to bind John was never intended to hold him; it was a complex set-up. A hidden accomplice (revealed to be a patient John genuinely helped, or perhaps an older character), or an unseen secondary mechanism, saves John at the last moment. John reveals that the key figures in the scam (except for Cecilia) are killed or incapacitated in the final, gruesome trap.

The film concludes with John and Amanda walking away from the scene. Cecilia, though technically surviving, is left in a horrific, inescapable predicament, realizing that she underestimated the man she tried to scam. John's faith in his Jigsaw work is fully reinforced, setting the stage for his subsequent games and cementing Amanda's role as his dedicated apprentice.