It's a meta-phor of how the fandom won't leave Scott alone and keeps pestering him constantly for new FNAF content. Michael/Creation and the Ignited animatronics are reflections of the most persistent fans who twist everything against Scott and even threaten him and his family should he not release more content. (And don't try to pretend those kinds of fans don't exist.) The game is a reflection of Scott's psyche as the fans continue to pester him, their demands warping, their hunger for more content growing insatiable, until finally Scott breaks under the incessant pressure (hence the ending) and gives into the fan's demands, now a thoroughly broken and melancholy man, and possibly commits suicide via house fire to make sure they can't make him keep going. The various newspaper clippings are just misdirection, and Michael really was a crazy homeless guy who somehow pushed Scott into his psychological breakdown. The constant repitition of "come back" is the fans pestering Scott. As for Nick's narration? It could easily be construed to fit with the above, and as for the Bad Ending cutscene? Perhaps Adult!Nick decided to follow in his father's footsteps...
Some of the fans who genuinely care for Scott's wellbeing (or just the ones who wanted him to not utterly destroy the franchise through sequelitis, your pick) decided to make the Ignited animatronics to scare him and turn him away from making more FNAF content, hoping that it would help him in the long run and make him a happier person, since he'd have time to make the other projects he wanted to do. Endless Mode isn't what it seems- it's actually the creators testing the animatronics to make sure they wouldn't hurt Scott, since all they wanted to do was give him a scare. (If one of them had been killed, they would've realized it was a bad idea. Nice Job Breaking It, Hero!) Since the testers didn't die, the ringleader of the operation gave it the go-ahead, and they shuttled the animatronics to Scott's neighborhood to kick off the operation. They didn't want Scott to blame himself for the events, however, and they didn't want to accidentally put anybody in danger, so one of their number, who was coincidentally named Michael Schmidt, decided to be a scapegoat and make sure the Cawthons blamed everything on him. He broke into their house and pretended to be a crazy amnesiac hobo, taking advantage of their kind nature to stay in the house and carry out the operation from the inside. Once the robots were released, Michael took position and told Val and Nick how to survive, but slipped up with Val by accidentally mentioning Scott's name and hung up in a panic. Instead of helping Scott, Michael personally oversaw and orchestrated Scott's scares, railroading him into going to the office for irony purposes. Some of the fans who want Scott dead (and they do exist, don't try to tell me they don't) moled their way into the little group and rewired the robots for murder, even making some of their own. They even managed to set up a kind of Bookcase Passage-styled system to make poor Scott lose his mind in the basement, but Michael figured out what was going on in time and diverted Scott to the attic in time, suffering the horrible mind screws that the crazy "fans" set up in Scott's place. The crazy "fans" sicced their own animatronics on Scott, deeming the original Ignited animatronics not efficient enough and cobbling them together into Creation in what they thought was a clever, ironic play on Ennard and setting the house on fire to leave no evidence behind. Scott, amazingly, managed to survive, but was killed anyway by one of the crazy "fans." (They didn't go after Scott's family because they didn't blame them for anything.) The original fans who started the operation to help Scott went into despair, and Michael, who already felt pretty guilty and wasn't the sanest after the mindscrewery of the basement, used some kind of spirit magic and managed to help Scott repossess his old body with the knowledge that it would only hold on long enough for him to say goodbye to his family. The line at the end, which seems to be from Creation, is actually from Michael, who completely lost his sanity in order to bring Scott's spirit back for a few minutes and has completely forgotten which side he was on in the first place.
Creation was an amalgamate of all of the other animatronics, and Mike claims they did this because they were wearing down. If Scott had managed to evade Creation until it followed suit, the haunting would have ended; the ignited animatronics would not have had any bodies to work with. The only threats left would have been Golden Freddy, who really can't actually do that much on his own, and whatever remains of the Fallen, assuming they weren't further-broken forms of the other animatronics.
He says, "Thank you for your cooperation, Scott Cawthon. I'll take everything from here." This isn't Michael talking at this point- it's Nikson, the creator of the game, speaking to our timeline's Scott Cawthon, thanking him for making the games and reassuring him that he doesn't have to make another game if he doesn't want to. When he states that he'll "take everything from here," he's actually referring more widely to the community and that they'll continue producing good fanmade content (no, that's not an oxymoron) for his sake.