My theory: At the end, Master Chief will discover that he is actually stolen enemy (What're the bad guys again?) technology and that the war was instigated very much as a result of this theft. One of the game's final battles will be Master Chief versus himself in a warehouse full of clones, a po-mo nod at the success of the game's multiplayer component.
Master Chief is the byproduct of ONI's top level bioengineering genetic/cyborg programs. The MOLINJR armor has also been through MANY revisions and is, aside from the shield unit installed on the MKII suits, entirely earth born. If anything I am far more interested in whats up with Cortana. First off it was indicated in Fall of Reach that she knows Spartan 117's (Master Chief) past and for that reason is willing to protect him at the expense of herself. Add to that the fact that SMART AI only have a lifespan of 7 or so years and Cortana guessed that taking in and holding the stolen data from Halo, which changed her, may have even shortened that life span. So I expect to see some tear jerkin sacrifice!
Also I find it weird one of the Halo 3 maps has 117 tacked on after the end. AFAIK Reach was the only place that was home to Master Chief, so maybe its just a nod or something but I find it weird every time I see it.
