Maybe I’m remembering something wrong, but I thought John said something just before he walked into Scorpy’s cell to the effect of “You bastard. You set me up. Not that it matters.” Then John walks up to Scorpius and spills his guts.
What was that all about? Did John somehow connect Scorpius to the flashback?
Did he mean that by following Scorpius’ suggestion to take the neural clone out of John’s head, it wouldn’t help to explain things further – keeping John in the dark and, thus dependent on the original Scorpius?
Was he not referring to Scorpius at all? Maybe the black-eyed traveler from “Unrealized Realities?”