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Turns out the device Jul had the scientist working on was a terminal to the Domain and a mini-Compiler.
Jul compiles Thorne into a Promethean Knight. But Thorne still retains some remenants of his personality and memories so he re joins the UNSC. Possibly after being directed against his old teamates by Jul.
And the Didact is hinted at. Turns out he was compiled as well and is not an uber Promethean Knight, crazy and insane but still a dam powerful and uber smart.