When you defeat subject Alpha he talks about wanting the locket you have back. This is strongly hinting that he is a clone (or some version) of Shadow. At the very beginning of the game one of the terminals says "subject Beta released". On my first playthrough I thought it was referring to someone else, but I'm pretty sure now it's talking about you, Cyber Shadow.

So it seems there were two different versions of Shadow made, the Alpha and Beta. There's another interesting terminal in a secret area in the research labs, which says "Incubation chamber A... status: breached" and "Incubation chamber B... status: specimen relocated". This would explain why you wake up where you do, for whatever reason Cyber Shadow was moved away from the labs to the underground cave where the game starts.

There's one more terminal that might be related to this. In the research labs computer room, one of the terminals (Hagan's personal log) says "The vessel attempted to restart an incubation chamber. To what end? Her life was obliterated... what could she be planning?" This might suggest that the AI copy of the Master was trying to bring back Shadow (for understandable reasons), which unfortunately resulted in the thing that was subject Alpha. It makes the AI copy's story even more sad.

The final question is, are both Alpha and Beta "real" Shadow, or is Alpha just a fake copy like the Master copy was? It's safe to say Beta is the real deal since his essence separates from the cyborg body at the end of the game. But it could be possible Alpha was real Shadow too, kind of like L-Gion was split into multiple robot bodies.

EDIT: On thinking about it more, maybe the reason why Beta was moved away to such a remote location was due to the vessel attempting to restart his incubation chamber (as mentioned in Hagan's log).