Does it do it with any other CPU intensive games?

Have you opened the case and put your ear up-close to the fans and HDD?

If you are still none the wiser, you can test your fans by applying a little pressure to the centre with your finger to slow it down and see if the noise persists. I do it to my fans to assess with one is making the most noise. I don't think it damages them since it's just magnets turning it.

The longer solution to see if it's your HDD would be to try defragging the HDD and start it up again.

And the most disruptive would be to reinstall the game. Don't know if that'd mess up any skins or saved games tho.