I've never played Halo (except a brief deathmatch at a con, which was surprisingly playable considering I've never used a controller for an FPS before). I've never even played Marathon (the Mac-based Doom contemporary by Bungie). But my friend has, and from what he's told me the appeal isn't just the running around with guns, it's the alien culture.
Now, I don't know much about the Covenant. Heck, I can't even remember what the difference between a phfor and a svit is. (Did I put enough 'phf' in there?) But I do know that Marathon actually managed to have a plot beyond 'shoot aliens', complete with kidnapping, rampant AIs conspiring against one another and against million-year-old alien empires, and some serious ambiguity about the identity of the protagonist (Mjolnir-class cyborg, anyone? I'm told you don't figure it out until, like, three games into the series).
I expect that Bungie managed to put something decent together for Halo's Covenant. Thus, you could well have a great resource for an alien menace to be plugged into any setting with a GURPS book.
Then again, I know absolutely nothing about any of this, so why am I even bothering?