Currently planning an AU, I already have the whole "Gregory is Patient 46, but doesn't know it" thing down for it. Basically Glitchtrap was completely in control and used him to get into the Pizzaplex. The plan is to hop from a vessel he has complete control over to the mainframe of the Pizzaplex. If he has control over Gregory still, that's great, but in the end he doesn't care. Sure enough, Gregory is free as soon as Glitchtrap leaves his body, so he has to kill him to keep his secrecy and sends Vanessa to do just that (with Vanessa as head of security Gregory being backstage where he's NOT supposed to be wouldn't be reported on). But Glitchtrap's hop into the mainframe did more than free Gregory: Glamrock Freddy had a Windows crash as a result, meaning he's free now too. Cue Security Breach.