The full plot of Saw 3 is two games running side by side: Jeff walks through a decaying meatpacking plant, while Lynn tries to keep John Kramer breathing in a hideout nearby.
Jeff's tests all involve people he blames for Dylan's death. In the first, he finds Danica, the only witness to the crash, chained in a freezer, but she dies before he can free her. In the second, he saves Judge Halden, who gave the driver a light sentence, from a vat filling with rotting pig carcasses. In the third, the driver, Timothy, is locked in a machine that twists his body, and Jeff cannot reach him in time.
Meanwhile, Lynn performs rough surgery on John to ease the pressure on his brain, and she keeps him alive. She begs Amanda to take the collar off, but Amanda refuses. She admits she has stopped believing in John's ideas and that she rigged her traps so nobody could win. Amanda shoots Lynn just as Jeff arrives, and Jeff shoots Amanda dead.
John then reveals that Lynn, who is Jeff's wife, was Amanda's real test, because he would not let a killer carry on his work. Jeff is offered a last choice between calling an ambulance for Lynn and taking revenge on John. He cuts John's throat with a power saw, and that sets off Lynn's collar.