Now, looking at the fly-through I am thinking that the 2 games should have different gameplay - Jacks story has to be in sequence I think. Start in Training head for the Carrier, learn about Fort and then make your way to the pier. But there won't be a Doyle to pick him up ... so we would need to send him over to Control. There he learns about the Archives and deals with Rebellion getting there. Since Valerie is dead he then needs a little incentive to hunt down Krieger - if there is that fight - I don't think Krieger as the popcorn muscled mutant was a good Idea in the first place. Much more meat in a story where he is eaten by his own creation, but thats for comrade roadie to decide (after convening with us of course).
So the end could be open - Jack dies in a last stand but we don't get to see that - (nomad will chance upon the skeleton with the red shirt...), or totally open - we just leave Jack at a key point. .... OR, Jack finishes the thing and comes back years later with a nano suit - nah, no good ... I say we bury him on that island and be done with it. Krieger should die too of course and the remnants of Krieger Corp (Rothschild etc) will initiate the link level Training, while the Nomad big level game could have its own kickstart incident - I actually know what and how but not telling
... I forgot to write about the other gameplay - the nomad one. So that would be the real Sandbox Game - unparalleled, the holy Grail - for the first time.... I can see the interviews and watershed events for the gaming industry when it hits home that one man and his Athlon64 put them all to shame. Big day.
Anyways - yes - the whole Archipelago turned into the Stalker like zone without radiation and funny spots. ...