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Much like Foxy and Freddy in FNaF 1, the Marionette in game is the mechanic that forces you to not just wait for your enemies to come to you, and close the door/hide. You have to wind it every X seconds, and if you are even a second late on winding it, you're dead. It will start playing "pop goes the weasel" and act like the original's "Toreador."

Story-wise, though, there are a series of minigames that imply that the Marionette is the one who put the spirits of children into the animatronics - Give them "Life" in a manner. There is also a possibility it either helped the guy who murdered the kids and hid them in the suits, or that it was what drove the killer mad enough to kill, as it is the only supernatural force that existed before the Bite/Murders.

This does assume you believe the events of FNaF 2 to either be a prequel, or a case of history repeating itself. There are also those who claim that in FNaF 1, there are wires around that could imply the Marionette/Puppet playing puppetmaster with the original group.