I would be really grateful if you lot would read all of this, and not skim any bits, as i know it's a bit longwinded. I stand by my previous thoughts:
It starts off with gordon hunting somewhere for a specimen of some type or other of the venerable anomalous material, possibly on a distant planet such as wherever the opfor aliens came from, and embarks on what develops into a more difficult mission as the aliens try to keep it from him. As he goes, he uncovers more about what happened to black mesa in his his absense (he hasn't been back since), and why the aliens want it so much. It emerges that there was another "white mesa" somewhere in the frigid polar regions of earth or on an ice planet, and it is there that gordon travels. He finds adrian sheperd in a state of suspended animation or whatnot, and once freed tells gordon of all that transpired, specifically the nuke. At this point they realize that the whole earth has been invaded by aliens. But, joy of joys, there is a time displacement facility!! So either with or without sheperd, gordon battles his way to the time transporter (on earth, in space, wherever) and returns to black mesa before the bomb goes off, and confronts the final threat that may or may not have been apparent in the other games. The g-man could have a shocking role in all of this, maybe as the guy who sold earth out, and sent gordon off into space whilst he was planning the invasion. But in the end, gordon finds a solution, prevents the bomb going off, and celebrates with a nice drink.
Whuf.......