Of all of the things to discuss in FNaF, the one topic that no one is certain on is the purpose of Midnight Motorist, mainly the "secret section" of the minigame.
The story goes that before you finish the final lap of the game, there is a black box at the bottom screen that you can enter. Going there will lead you to a different section where you drive the same purple car as before. You can exit out of three areas, one being a location called "JR's", the other is a more obscure area where you find a pile of dirt, and the final where you enter your house. Whenever you exit your car, you find that you play as a yellow figure, this will lead to the confusion that will be discussed later.
Upon entering your house, you'll find a person watching TV saying "leave him alone for tonight. He had a rough day". You ignore this and walk up, the yellow figure find a locked door and say "I told you to not close your door. This is my house, he can't ignore me like that. OPEN THE DOOR! I'll find a way in from outside...".
You leave for outside and find a broken window, a large set of animal footprints and a trial of tiny footprints. The yellow figure will end the minigame saying "Ran off to that place again. He will be sorry when he gets back".
Sound simple enough, but the problem is that no one knows when this event happened in the timeline, who the characters are and what is going on. While I do think that MatPat helped to solve it in one of his videos, I think I can add more onto it.
I think that the yellow figure we are seeing is actually William Afton himself. It might sound crazy since his 8-bit sprite is not purple, but there are a few things that point to that.
First off, in both the main part and the secret section of Midnight Motorist, you control a purple car. This is the same purple car seen in FNaF 2 after William killed Henry's kid outside of the restaurant.
The second is that in both the secret section and the final part of the Security Puppet minigame, it's raining with not just the same textures used, but also the same ambient rain sounds. By the time the Puppet got out of the building, William got off the highway.
The third is in said Security Puppet minigame, if you brighten up the final screen, you'll see tire tracks. This reflects the ending of the "Take Cake to the Children minigame" where William drives away after committing his murder.
The fourth and final is that the secret part of the Midnight Motorist section is called "later that night" in the MFA.
These details put together help to paint the first picture of this minigame.
After William killed Henry's daughter, he quickly sped off for home later that night, meaning that Midnight Motorist happened right after the Security Puppet minigame. So now with William's presence and the timing of events established, let's look at the other parts of this confusion minigame.
The second thing we need to get out of the way is the other characters in William's house. When you get home, you'll find a person watching TV, and you'll see reference of another person that "ran off to that place again". This establishes the presence of two people who are connected to William.
I believe that the person watching TV is Michael Afton. In SL, he watches TV after the end of each night. If that Yellow Man is William then this makes sense, as Michael is William's kid. Furthermore, Michael has a younger sister named Elizabeth, as we see in SL. Though who's that other kid that William mentioned who ran off? That makes Michael having two other siblings, especially since this person who ran away is describe as "he". It was commonly believed that the other kid mentioned was the Bite Kid. It was commonly suspected and seemed to be backed up in Step Closer that Michael Afton is the Foxy Brother, so this makes the Bite Kid the one who ran away.
Though where DID the Bite Kid run off too? It could be Fredbear's Family Diner. MatPat pointed out in his FNaF 2 theory video that the Puppet murder occurred at Fredbear's, which is something that Scott did not debunk at the time he released FNaF 4. That's the same game where we see the location and is the same place that the Bite Kid did not want to attend for his birthday. This alone explains WHAT the Bite Kid saw at Fredbear's and why he was crying all the time; he found the corpse of Henry's Kid, there was a murder done at a place he used to love. This is why William said "he will be sorry when he gets back". He IS sorry for what he found.
With that said, the other thing that I don't think many people noticed is that despite the presence of Michael, the Bite Kid and William, Elizabeth Afton is nowhere to be seen in that section. No reference or mention of her (not even from Michael when he talked about the Bite Kid). She's just not there. Elizabeth may have been dead at this point. This might contradict Cassette Man's dialogue where William "first inflicted a wound onto him", but if you consider that the Puppet murder happened before "later that night" and the fact Elizabeth is no where to be seen, this could be an oversight on Cassette Man's part.
So, where is Elizabeth? Do you remember that pile of rubble that you can find? William strangely makes no comment on it, and it's odd as to why it was there at all. I believe that pile was a fake grave site for Elizabeth. Remember that Elizabeth was dead for a long time and wasn't "put back together" until the events of SL.