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Glitchtrap has something to do with Tony's Dad's arrest.
The intro of the story has the teacher saying that, specifically, their mystery is supposed to have a bunch of "seemingly unconnected" plotlines that all end up being necessary to reach the final conclusion. Seemingly, the only real plotline that ends up contributing to the GGY mystery is Tony's friendship with his friends. The other subplot is his angst over his father being wrongfully imprisoned, and how his dad made him promise not to investigate out of fear for his safety. His dad worked for a big company and supposedly embezzled millions; meanwhile, we know GGY is an expert hacker who's able to go undetected by the tech geniuses at Fazbear. It's possible that GGY and Glitchtrap/Burntrap were the ones who embezzled the money as part of their plans.