Poppy Playtime has built up a lot of mystery around the Prototype. Players can find VHS tapes that talk about the Prototype and the danger he poses to the researchers, having killed at least one of them in an attempt to escape. Though there hasn't been a lot of information about the Prototype, there's enough to theorize about his identity before he was turned into a toy.
[Warning: This article contains spoilers for Poppy Playtime Ch. 2.]
Poppy Playtime takes place in an abandoned Playtime Co. factory, where the player is an ex-employee looking for answers as to what happened to their former coworkers who vanished a decade ago. As the player explores the building, it becomes obvious that Playtime Co. harbored some dark secrets, and that they experimented on both adults and children in an effort to create living toys. For all the lore that Poppy Playtime revealed so far, the identity of the Prototype and his motivations are not among those revelations and continue being one of the game's biggest mysteries.
The Prototype is also known as Experiment 1006, which players mistakenly thought was Huggy Wuggy in Poppy Playtime Ch. 1. A note in Elliot Ludwig's office from Poppy Playtime Ch. 2 says that experiments in the 800s were being done on animals, not humans. It's possible that the Prototype was among the first successful human-to-toy transference processes.
The Prototype As A Playtime Co. Researcher
The snippets of information about the Prototype in Poppy Playtime give crucial details to putting together the mystery of his identity when he was a human, and that leads to hints as to why he ended up as a toy that seems far more malicious than the other toy monsters. The process through which humans become toys at Playtime Co. is not entirely clear aside from the fact that it requires the use of poppy flowers. However, traits that the subjects possess carry over in their transfer to becoming a toy, sometimes with additional hostility, but that is a key factor in identifying the Prototype.
One of the main complaints the researchers had with the Prototype in Poppy Playtime is his lack of obedience. In combination with his high intelligence and ambition, the Prototype is a menace, and he was likely one of the high-ranking researchers at Playtime Co. when he was a human. Intelligence and ambition are key qualities for any supervising researcher conducting complex research like resurrecting the dead as toys. The Prototype also has a strong understanding of the research facility, like a researcher would. He knew how to disable the camera in his room, and how much time he'd have to hide in its blindspot afterward to attempt to escape when the researchers came to check on him. Not many people would have had the knowledge required for that plot.
Poppy Playtime Ch. 2's ending sets up the Prototype as an antagonist, if not in the next chapter, then a future one. All the information given about the Prototype so far lines up with him having been a researcher while he was a human, and those traits and experiences will make him a formidable enemy. The remaining question would be why the Prototype took part in the experiments if he is, indeed, a former researcher in Poppy Playtime.