Ok, so... I made my first theory, but now I have some more to add on to it.
First, is The Prototype, aka Experiment 1006. I was wrong bout thinking he was Elliot child. That’s just because he IS Elliot Ludwig. The game talks about how Elliot Ludwig donated his body towards the research, therefore merging his body with one of the toys. This explains why 1006 has the bones molded into his framework. I also think, credit to superhorrorbro/ evidence found in game, that Elliot Ludwig isn’t evil. And it explains quite a lot more, too. Elliot Ludwig wasn’t an evil man, always testing his experiments of ressurection on small animals, those of which were already dead. He never believed in the killing or murdering of anyone, he wanted to bring things/people to life, not end theirs. Once he donated his body to the creation of the Prototype, a new team took over the running of the laboratory. But, they had something else in mind. The new team then set up the Foundation where unsuspecting workers would drop off their children at the Game Station, not realizing that they would be suspected to testing. The three games, ( Musical Memory, Whack-A-Wuggy, & Statues) would help the scientists observe and test the children. It would also tether them into each of their assigned toys, making the ressurection process easier. (Poppy Playtime was most likely Elliot Ludwigs deceased child, who was ressurected as the doll she favored in childhood, meaning she had some-type of physical/ emotional bond to it). The tests would tether them by scaring them, forcing them to rely/ bond with their assigned toys. I think it also slightly prepared them to the ressurecting/ toy creation process, ( notice how in Musical Memory, the words ORANGE and VIOLET sound quite like ORGANS and VIOLENT/VIOLENCE, and how they added MASSACRE too, huh?). Now, it is quite possible that Elliot Ludwig wasn’t to fond of this. He was against of what they had turned his dream into, eventually escaping and running rampant around the factory, killing all the unsuspecting employees, and some or a few of the helpless toys. We can assume he got the other toys in on the action, as the last tape in Poppy Playtime Chapter 1. In the tape where everyone is dying in the background, you hear the scientist mention that the Prototype, aka 1006, shows the ability and is fully capable of co-operation, and coordination. He was able to coordinate an attack on the employees, killing them all as revenge of what they turned his dream into.
