| d20 CoC uses more or less the same d20 system as d20 modern. I'd expect d20 modern to be slightly more survivable, depending on how much of the tech you give the bad guys.
That said, Delta Green is basically exactly what you describe. Basically, the events of Shadow over Innsmouth happen as described, then the OSS forms a team of Mythos fighting agents. At some point, the group goes rogue and officially doesn't exist anymore. However, it continues to get support.
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All we want to do is eat your brains
We’re not unreasonable; I mean, no one’s gonna eat your eyes
All we want to do is eat your brains
We’re at an impasse here; maybe we should compromise:
If you open up the doors
We’ll all come inside and eat your brains | 
And yet another word from our sponsors
