Foxeye, did you look up the cut final mission on youtube? It explains a little more and shouldn't have been cut (or rather they should have let the team finish the game instead of rushing a release).
I'm not sure it explains anything. It just puts you back at square one, really.
That's all this game does story-wise. Goes round in circles and ends back where you started.
It was deeply unsatisfying in its conclusion. Whichever conclusion you choose.