Why are there ads all over IE and Google Chrome? How do I fix this?

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Ok, just recently I've been trying to find the map maker mod for the game: Yuri's Revenge.
The map maker is called: Final Alert 2: Yuri's Revenge. Well, I kept getting bad downloads and stuff that I was not looking for and tried to delete the files as soon as possible. Then lately, I noticed that there were ads all over IE and Google Chrome (some are from Smarter Shopper and the others are from AdChoices) The ads from AdChoices I've seen have been floating over text on websites and covering it up slightlty. I cannot figure out how to get rid of this or what could possibly be causing this.
In conclusion, can someone help me fix this whole issue? Please be specific and show good evidence that the possible fixes will work flawlessly.
(How do I fix this permanently?)