The Queen of Maggots resurrected John in the same way that she did Lorelai more than once.
John looks very dead after he gets his head slammed into the toilet seat, and it also seems like he should definitely be dead after having an entire shipping container dropped directly on his head in the factory. So how does he keep getting back up? If you think about the Queen's motives, it would make sense for her to bring John back to life to oppose Lorelai in the short-term. That way, Lorelai keeps getting killed and she's desperate enough to do what it takes to get back to the real world again, opening the door for her to become the Princess (and eventually new Queen) of Maggots. Plus, John only stays dead once Lorelai has killed the Queen of Maggots herself. Coincidence? Perhaps not!
The Queen of Maggots was influencing John's actions, just like she wanted Lorelai to influence Al.
Even if the Queen of Maggots wasn't directly resurrecting John (maybe he's just THAT resilient), she still could have played a larger role in his choices than she lets on to Lorelai. One of the biggest complaints people have about this game is that John's characterization seems too one-dimensional and irrational. Why does he suddenly go on a murdering spree? It does make a little more sense if you imagine the Queen of Maggots being the devil on his shoulder, much like Lorelai is for Al (if you play it that way) in the 5th chapter. She tells him that he'll go to prison, that it's the family's fault anyway for not valuing/loving him enough, that they deserve to die for ruining his life...and it's enough to push him over the edge.
Lorelai being too late to save Zack and Bethany in the factory was engineered by the Queen of Maggots.
The game has multiple characters insist that time is "frozen" when Lorelai is dead, but that's shown to explicitly not be true! It's definitely moving much slower than time in the afterlife, but it's still moving nonetheless. The most egregious example is the second time Lorelai comes back to life. In the interim from when she was dies to when she revives, John has had time to find and incapacitate Zack, transport all of the bodies out of the apartment and into the police car, drive them to the brick factory, move the bodies into the shipping container, and outright murder Zack/Bethany. All of that HAD to take at least a couple of hours. So Lorelai having "all the time in the world" was an outright lie from the Queen Of Maggots, and it goes further than that - maybe she even had control over exactly when Lorelai revived and purposely placed her right when it no longer mattered (while also making it seem like just a tragic inevitability instead of her own cruel design). This theory even works in both outcomes of the Al chapter, but for different reasons.
In the "Al lives" story path, the reason for doing this is pretty obvious. The Queen of Maggots is punishing Lorelai for going against her will by following through on her threat. She never said she would kill Zack and Bethany outright, after all, just that their lives would be forfeit.
In the "Al dies" story path, after being told that she will have to become the next Queen of Maggots after killing John, Lorelai says that she wants to stay with Beth and Zack. At that point, the Queen of Maggots realizes they're holding her back and that if they're dead, Lorelai doesn't have any earthly connections left, which should make her less willing to resist her "destiny." Better yet, the Queen of Maggots can play off their deaths like a tragic happenstance that couldn't be avoided instead of something she specifically had a hand in.
