SUPER MASSIVE SPOILERS.
PLEASE STOP READING, SINCE ILL DISMEMBER THE WHOLE PLOT.
I hope I'm not spoiling anyone and, if so, I'm sorry.
So, here is the thing. Lost Alpha does MUCH BETTER at telling the story (and it changes it severely) BUT... there are a few things that do not add up.
a) There are a total of (that I found) 2 encounters with an "allegedly" SIN guy, with no name (or .... as a name). First, it appears outside the entrance of the bar bunker. I didn't kill him, so he killed the guards and got into it. Second, in X-14 (If I'm not mistaking the name, the lab with the "Doomsday device") after you stop the device. BTW... there are certain moments in the maze that were AWESOME. Specially once you turn that radio off that is in one of the rooms... WOW! I didn't kill him either. Also, you will see him in a vision when you get to Doc into the swamps AND once you find the Monolith.
So, who exactly... or what, is he? I know he can be killed because I tried once (although I reloaded. So, I didn't kill him in any of the encounters), but there is no information about anything at all. And since he teleports on and off... and goes away if you don't do anything to him, he definitely isn't human. Or not anymore.
b) Once you get to the swamps (that chopper was a pita...), and have the vision, what does really go on on such vision? You see several "chess figures" arguing (can't remember exactly what they were saying, to be honest. Anybody care to remind me?), and finally one makes the others shut up, and the SIN .... with the cloak appears (or does it? Not 100% sure).
what is going on? I thought I'd find them... but I didn't.
c) Once you get into the Radar, and get into the final lab.... WTF?! You find "something" (a pyrogeist), that claims to be a "god"... but you kill him with pretty much everything you had and... thats it?! The game ends there?!
d) What is the connection with the cloaked mistery guy and the monolith? I know he appears once you find him....
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I get it: the Radar is what controls the Ionosphere (or whatever the name is for the one being manipulated) and, thus, controls the zone. Apparently, they were trying to do experiments on behaviour by manipulating certain layers around the earth. Meanwhile, they were working with giant brains (there are several throughout the game. Even in X-14 the Doomsday device is a giant brain)... and something went wrong and they created a self-conscious being.
BUT, where do the chess-figures come in? Do they come from other "zones" or experiments around the Globe? Why does the final boss, the "God", say close to nohing, and is so easy to kill?
I don't know. Something isn't as clear as it should be....
PS: kudos to whoever had the idea of the "Gordon Streaman". I almost cried of joy when playing that part. BRILLIANT!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!