Er...HL, NOLF, SS2, DE, T2, MP, etc.
On pure story, it is fairly average or just on par with everything else. Some supposed war that is never progressed or explained in depth, you are the loner combat dude, got left alone, fight mutants, ring system that was never progressed or explained in depth, and kill big bad guy.
What really makes a game great is how deep the story may or may not be, how complex or dynamic it is, how well it ties into the overall gameplay, and, ultimately, the sense of progression and/or accomplishment.
If you want to discount all the FPS games and focus on just FPS, you would have to discount Halo
as well and give the award to Serious Sam
or one of its clones. After all, they keep the "FPS" store pure: KILL STUFF!
was a bit misdirected with the "popcorn" horde and repeat levels,
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