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. ...
Let's step back and think about the whole project - we have the archipelago and the background story of a mad scientist creating the Trigen zombies in his quest for the nano skin funded by the CIA and guarded by Mercs. Jack Carver happens, the Trigens break out, Labs get locked down and scientists are ripped apart trapped with their own creations in these AI governed tombs. Valerie dies, Jack dies, Krieger dies and Doyle never existed.
Let's take the Koreans out completely. 2 Factions, Trigens and Mercs and the Mercs, on retreat, leave the fighting drones in place to guard the 'Zone' and hunt down any remaining Trigens. Let's forget about 'recreating' the Jack FarCry missions for the moment too. The research or what was salvaged of it is continued elsewhere and the NanoSuit is the result. The Islands are cordoned off by water mines and defence drones out at sea with the mobile drones roaming the islands maintained by remnants of the Merc force.
Years pass and Legends turn into myths.
So FarCry reloaded is the Nano Suit meeting its 'Father' the Trigen. The trigen project Krieger initiated grew Nano Skin on dead bodies and achieved the 3 states of Armor, Strength and Speed. Cloak was added much later in the final Nano Suit when the horrific practice of creating zombies to 'grow' the skin could be abandoned through scientific progress and the whole project was moved and rebranded in the States.
Let's say the Mercs and their drones can only hold a balance of power on the islands - contain the threat but not eliminate it and therefore are not able to go deep into the abandoned labs. The remnants of the Krieger Corporation however are interested in some artifact or whatever deep inside one of the core labs without knowing the exact location.
So the raptor team is dispatched to end the trigen menace and some top notch mercs are dispatched to find the artifact thingy. And this happens at the same time.
Krieger Corp and the CIA are basically on the same side and Pentagon sends Raptor unaware of their plans. But they are aware of raptor and that brings about the opening sequence of the game leaving the player stranded on the island and not even knowing what the mission is...