This post was just made to clear up some confusion on the lore that is presented in game, as I think it's already time I explain some details:

There are many bits I want to clear up in the File Menu, so, here you have it:

Every DEHS model is given an associated subject, however, it seems not many people seem to catch this, but the subject always displays "deceased x months ago". This means the subject used was already dead by the time they got put into the model. Basically, they were digging up graves, doing techy stuff and putting the bodies into robotic beasts.

On "Model 3 Tests", it shows it shows Model 3 was unable to recall memories from the past, but it knows what a human is, and, by proxy, it understands what it is, she knows she's human or at least supposed to be.

On "Termination", a "boy" is mentioned, this is Jeremy. Yes, no beating around the bush, that is him, the flesh bits attached to Model 3 are Jeremy. Also, she willingly attached the flesh to herself, why that is I can't tell.

The Prototype in its original state was just a simple metal endoskeleton and completely unable to move as the file says (which, btw, they are all telling the truth). However, in game, it's covered in flesh and able to move, somehow.

Here's a transcription of what is said on the TV in the cutscene just before the boss fight, in case you didn't understand:

"Hello, I" Shows image of tube containing Model 3
"We" Shows heads of the three animatronics.
"You, HUMAN"
"We, not HUMAN, why?"
"Help we, you, help, we need help, we need you, we need human, human, human, human."

When William Afton presents himself, a Rabbit animatronic shows up, that Rabbit Animatronic is William Afton himself, as he implied he was coming to get you. However, that animatronic might seem familiar if you played the previous game, Distorted Mind: The Other Fredbear's.
And, on that topic, yes, this game is a sequel to The Other Fredbear's.

The overall narrative is centered a certain theme and the character of Model 3 embodies that theme. Even the name of the game "True Humanity" relates back to her belief and her goals.

Lastly, what happened to our player character? What are we supposed to understand from the ending? Well, the story isn't finished just yet, so you'll have to look forward to the future.

Hope this clears up some doubts without revealing too much, I want you to still put it together after all!

EDIT: Oh, also, happy Valentine's Day I totally forgot about that.