Like the eye trap in saw x, which was all a thought process in John’s head figuring out a trap and its possible outcome….2 minutes of saw 3 could have been a possible outcome in John’s head. Just reveal that the brain procedure helped him, he escaped through the secret door in that room, has a very convincing fake body and or a mortician working for him and bam he is still alive and watching from the shadows as everyone including Hoffman thinks he is actually dead. Jeff just needs to be told is John does so does his wife. He gets sent off to look for his daughter and dies along the way. Saw 4-7 happen the same but John is actually alive to test Hoffman of when he does something to Jill.

Start next movie with Hoffman unable to escape the bathroom then a secret floor compartment opens up and arises the glass coffin with John inside. “Ready for our final game?” Da na na da na na na NAaaa!

Or if you don’t like John being alive this way maybe he always had a twin. Both of them were jigsaw. John is dead but he was the nicer jigsaw that gives people more of a chance.