Never mind the details. The way forward is simple enough to one with a disciplined mind.
There's no way he can possibly navigate the mess of distorted memories and glitchy neural augmentation well enough to plot a course forward as far as mission objectives go. He's got no way to contact headquarters, or at least no way to make sure that it's really headquarters he'd be contacting. He's pretty good at knowing when someone isn't who they claim to be, but he simply can't trust himself to know when somebody really is who they say they are. In a way that makes things simpler.
He will kill his contacts. Every last one of them. This will demonstrate to headquarters that he can't be trusted to perform operations, and as a result the only people trying to contact him will be enemy spies. And he's never felt conflicted about killing enemy agents.
He knows his handlers will understand this behavior. It's the kind of logic they've always promoted. They won't hunt him down for this, but they might try to find him eventually. He'll know he's dealing with his true agency when they bring him back to the city in the sky. The one in his dreams. Until then, the chain of command is as empty as the holes in his memory....