My friend and I have been spending many hours poring through FNAF files, including FNAF World and The Silver Eyes, and thanks to the content Scott has released through these, we have come up with a pretty good theory. This theory makes almost everything in the FNAF storyline make sense, which is very hard to do. I didn't want to keep the theory to myself. I wanted to share it with other people in the fandom to discuss it.
Our theory begins when the storyline does, with Henry and William Afton meeting each other. The two, as we all know, become great friends and business partners and open Fredbear's Family Diner. Henry is the sole creator of most of the animatronics while William handles the business aspects of things. William is obsessed with Henry. He expressed violent jealousy and borderline worship of him in documents the police found in his apartment after the 5 murders. I believe the obsession started immediately. William has two children, Michael, who I believe was between 11 and 15 years old at the opening of the Diner, and a daughter who I think was 1 or 2 when the Diner was opened who I refer to as Baby. Henry has identical twins, Charlie and Sammy, who were around the same age as Baby. Henry has a wife, but it's never said whether William does or not. Due to this, I think Baby and Michael are stepsiblings. At the Diner, William sees an opportunity to make more money. I do not believe he was evil yet, although he was obviously very crazy. Henry made Circus Baby, who is referred to in FNAF World as a "terrible mistake he cannot deactivate." William obviously designed Circus Baby, that's confirmed in the beginning dialogue of Sister Location. I believe William knew what he had done when he designed Circus Baby, but Henry didn't realize it until he had already activated her. She was sentient from the point of activation, so deactivating her would've been pointless. I believe Circus Baby was kept in the back of the restaurant for a little while before Circus Baby's Pizzeria opened. In this time, the night of Oct. 31, 1982 came. This is the night in The Silver Eyes where William kidnaps Sammy. Henry and Charlie left the restaurant soon after this happened, but William kept it open, which Henry most likely knew. I was confused as to why Sammy was taken the year before he was killed since he's obviously the kid in FNAF 4, but then, it dawned on me. In the book, Charlie says that William stood there for a while trying to decide which one of them to take. He picked Sammy. But why? It's because of his obsession with Henry. Taking Henry's son gave him a chance to make his own Henry. That's why he didn't die immediately after he was taken. William was raising him himself. In the time between when Sammy was taken and the time that he was killed, which I believe was exactly a year (it refers to the day Sammy died as his "birthday" which would make total sense. William considers the day he took him as his birthday, and I believe it was on Halloween since the game release date was originally Halloween, the game was the only one with Halloween themed DLC released for it, and the kids were wearing masks, so they were dressed in costumes), Circus Baby's Pizzeria was set to be opened. In the few days before it's opening, Baby begs Afton to see Circus Baby. Circus Baby reveals that she was only on stage for 1 day, so the restaurant was closed a day after opening when Baby was killed. It would make sense for William to not be watching her, he was dealing with the grand opening of a restaurant and was likely very busy. I also think that both Michael and Sammy saw Baby get killed since they were most likely at the restaurant with their father. This explains why Sammy was so scared of the animatronics and why he wouldn't go back to certain parts of the restaurant because of something he saw. They closed the pizzeria, which was attached to Fredbear's through the red door above ground. After Baby's death, William moved the pizzeria underground and it was still connected to Fredbear's. William most likely blamed Michael for his sister's death, making his hatred for his son grow (I think Michael was the illegitimate child Vlad/William was refusing in the Immortal and the Restless). After this, Michael's jealously begins. He starts bullying Sammy because his father loves him more. This is the abuse we see in the mini games in FNAF 4, its Michael being jealous. Michael takes it too far and jokingly puts Sammy in Fredbear's mouth where his wiggling and tears cause the spring locks to malfunction and crush Sammy's head. William blames his son for Sammy's death as well and tortures him. This explains the events of FNAF 4, and why the only rooms you play the physical game in are seen on the SL breaker room map and not in any of the mini games in FNAF 4. This also explains why the lamps in the side hallways and the lamp in the living room in SL are the same. William built additions that could only be accessed by vents onto Circus Baby's Rental Service to torture his son by experimenting on him, watching him through the monitors in the private room with the code 1983. Michael seeing Fredbear with a mouth in his stomach combines the two deaths he was blamed for into one. Fredbear is vicious with large teeth for the bite Sammy died from and the mouth in his stomach is for his sister being pulled into Circus Baby’s body through her stomach. After this, the events of SL happen. William no longer cares about his son, so he sends him into the SL to get his sister because it’s technically his fault, and also because William knows he will most likely be killed. Michael goes because he's willing to do anything to make his father love him again. This is why he stays after he was kidnapped, he's determined to get his father's love. He's scooped by the animatronics and they escape using his skin. William (either before or after SL) goes with Henry after closing Fredbear's to open Freddy Fazzbear's Pizzeria. This explains the gap of time between Sammy's disappearance and Charlie's memory of when she moved into the new house in Hurricane. This pizzeria is open from 1983 to 1987. The 5 kids are murdered and the restaurant is closed. Henry kills himself shortly after (or maybe William kills him for knowing too much). William builds a new pizzeria in November of 1987, the new and improved Freddy Fazzbear’s Pizzeria. This explains why the toy animatronics are rougher around the edges and have many glitches. William is less talented at building animatronics than Henry was, but he had no choice but to build them himself. He either opened the restaurant in hopes of killing more children or making money. It’s only open for two weeks before Toy Foxy or Mangle bites the night watchmen Jeremy Fitzgerald. He lives the rest of his life without his frontal lobe. William takes the “old” animatronics to a different location where he tries to open another Pizzeria. The place goes bankrupt in 1993 and William moves the animatronics back to the first Freddy’s where they are sealed into the building by a mall. Nobody purchases the property, and William acts like a security guard to watch the place and stay as close as possible to the suits. Between the closing of the first Pizzeria and the murders in 1987, William is trapped in the Spring Bonnie suit and manages to escape, explaining why his eyes were dead looking, because he was actually dead. In 1997, the events of The Silver Eyes happen, and Charlie and her friends are trapped in the restaurant with William and are almost killed. They find out the children are in the suits and that William killed them to make a family of his own. They escape by trapping William in the Spring Bonnie suit again. He escapes a second time. The restaurant is left where it stands. Between 1998 and 2020, William sends Michael to the restaurant to his death. I think William sent Michael because he knew if he ever went there again, the kids would try to kill him. He sent Michael in his place. Michael is mistaken for his father and killed in the Spring Bonnie suit. Since he’s a literal hollow shell, he quickly decomposes. His soul, which was basically all that was left of him, haunts the suit. Fazzbear’s Fright, the horror attraction, is opened in 2023 (30 years after the closing of the third Freddy’s). The night watchman there is either someone who had been to Freddy’s as a kid or William himself. This explains the hallucinations of the animatronics. Only someone who was familiar with the restaurants could hallucinate the animatronics (Mangle, Balloon Boy, and the marionette are there so it very well could be Jeremy). The watchman burns down the horror attraction in an attempt to kill Spring Trap, or Michael Afton. He survives the fire (as seen in the secret cut scene after you beat Golden Freddy mode in the Sister Location Custom Night DLC) and promises to find his father.