What's wrong with my computer?

Yesterday, something went wrong with my laptop. I was getting these pop-ups saying I had a virus and that there was an intrusion on my laptop. The reason I didn't take it seriously was because I had gotten the same exact pop-ups several times and several months prior and yet nothing bad happened. Also, the pop-up warnings were from a different security system than I had(I had Avast and Sandboxie) so I thought it was just something to get me to buy something, which happened last year too. However, this is what happened. All the icons on my desktop and in my start menu are gone except for the recycling bin. So I checked there to see if my things were in there. They weren't. I don't know what happened. Can someone please explain to me what could be wrong?