In the very mini game the room is shown some dripping water in the ceiling, of which caused the spring locks to snap shut, impaling Afton in literally every part of his body, causing his horrific death. Considering that anything that dies or is stuffed in something, ends up possessing it, our pal always comes back, but is a horrific corpse inside of a old damaged suit. Now, since this pizzeria wasn’t closed, they eventually found out Afton’s corpse and instead of cleaning up the mess, just downright close of the entire room as if it did not exist. Now let’s go back to Micheal, after having literally everyone in his family die, he probably decided that his best course of action would be to undo all the problems his father caused.
He went to the first Freddy’s, where he was attacked by the robots, guess kids do resemble their murderous father’s appearance, of which he was able to survive by very obviously staying in the security office, and to make sure he didn’t get rejected for literally having a serial killer as his father, he used fake names, in this occasio, Jeremy Fritz, or something idk. At the end, he burnt down the entire restaurant in hopes that the spirits would be freed. Now I have no clue if these were the ones scrapped in the service room in fnaf 2, but they probably were. Michael then goes to this one, and does something with the robots, but didn’t burn down the pizzeria this time. I’m pretty sure the toy animatronics (the upgraded ogs not including mangle, mangle is theorized to have been possessed by Susie’s dog) weren’t possessed by any dead kiddies, therefore making it unnecessary for him to burn them down, but the restaurant did close down, most likely due to the Og robots.