Weird fps drop and rise

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A year ago, I was able to run WC3 fine w/o a graphics card. But when I play games like Civilization 4, Sims 3, Age of Empires 3, it was unplayable and exceedingly choppy.

I decided to get a graphics card and everything became smooth.

4-5 months later, all my games became choppy again, even WC3. It was still somewhat playable however. When I open a game, say Civ 4, it would be fine for about 5 minutes but then it was followed by 5 minutes of choppiness. This would continually alternate.

I noticed that when I start the CPU, there would be a very strange sound coming from the computer(Sounded like it came from the graphic card's cooling fan)

Few days ago, I got the SC2 Beta. The game would run on 10 fps that fluctuated by a margin of 2.

Now here is the strange part, I decided to minimize SC2 and Google why my FPS was low. But when I re-maximized SC2, the FPS ran at about 80 FPS with a margin of 20 plus or minus.

Whats with my computer, what can I do to make games playable?
 
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