In the Retro CD's, Patient 46 is hinted to be a child. This is because they're mentioned to be short and the therapists talk to them like that they're a child. This is a complete contrast to Vanessa's sessions, who wasn't talked down in the same way 46 is.

For a while, this theory was believed to be debunked because in all the official non-English transcripts of the Retro CD's, Patient 46 was referred with female pronouns (unlike the English language, certain words in other languages can be intermixed in with pronouns, like "mischievous"). This turns out to be an error as the Tales from the Pizzaplex story "GGY" reveals that Gregory is Patient 46.

With this theory being confirmed, this leads to the other theories below:

With the information that Gregory is Patient 46 and has a murderous streak, this lead to the belief that Gregory is secretly evil and is manipulating everyone with a false "innocent child" persona. However, Gregory has a genuine reaction to all the things in the game like as he saw them for the first time, including the animatronics being hostile and wanting to hunt him down, despite Gregory hacking the robots to make them act like that.

One possibly explanation is that Gregory was corrupted by The Mimic in a same way as Vanessa did. In Vanessa's case, she acts normal when she is not under the influence of Glitchtrap, but is aware of its presence. Given that Gregory never comments on this similar presence, it's possible that Glitchtrap was able to hide from him, or could have the ability to alter, destroy or block his memories entirely.

In the SD emails and Retro CD's, it's implied by some of the other characters that Vanessa is secretly working with someone.

This theory creates a bit of a bizarre plot hole, as neither Gregory or Vanessa recognize each other in Security Breach despite being in contact during the events of Special Delivery. Vanessa knows that Gregory is looking into her files, but refused to comment on it (despite Glitchtrap not controlling her at this point of the recording), as Gregory is the one who did the heavy work to take over the entire pizzaplex.

One possible explanation for this is that Glitchtrap has the ability to manipulate or destroy/block memories, which can explain why the two acted like they met each other for the first time. Or, it could be possible that Glitchtrap was behind the entire thing and switched back and forth between Gregory and Vanessa in order to carry out his tasks.

This theory seems to be more likely in the case of Ruin than in Security Breach. Prior the events of the DLC after The Princess Quest ending, Gregory and Vanessa went back to the Pizzaplex to seal The Mimic away by creating the M,X,E,S, system. Their intention is to prevent it from escaping or infecting anyone else, as the two were previous victims of the Mimic's control via Glitchtrap.

Fo

This theory seems unlikely due to the events of Ruin and The Mimic's violent demeanor being a result of the programming.

One other thing worth noting is that there's a scrapped line where Glamrock Freddy knows why Gregory he's not in the customer database and he remember him from some unknown incident, as his voice cuts off before he could finished. It could be possible that Gregory did something prior to the events of the game that caused him to get blacklisted, though it's never mentioned what it was. Outside of speculation, it could be related to him hacking the animatronics to make them become hostile or obey him, or killing the therapists because they questioned him too much.