First things first, protocols

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'll know he's dealing with his true agency when they call 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....