The story is quite good, and going through every web of intrigue target will give you some perspective on it all.
The few 'plotholes' are easily written off as cliches that happen in most games/movies. Here's a minor one, I'll keep it as vague as possible:
[spoiler:0f80b81930]
At one point, you're trying to get this guy. He's in a helicopter flying around an infected area waiting for the 'all clear' to be given. You run around destroying the infection sensors, so it looks like it's safe. His chopper lands within a few feet of you, and you just stand there as he notices the area is still infected.. and then just flies away. You COULD have easily ripped the helicopter to pieces right then and there, and had him... but you didn't, as that would have ended the story early.[/spoiler:0f80b81930]
Minor crap like that. Nothing that actually ruins it as a whole.
The gameplay more than makes up for that kind of thing.