Went away for an hour, came back all files were gone.

Ok, I worked on it for a little while, (ran a virus scan, found a few trojans, removed them) but I was curious, How in the WORLD is it scanning files that I don't see. The only thing on my desktop was the recycle bin, and a file recovery thing. So I clicked "Show Hidden Files" (after lots of thinking and crying and restoring[just one] to a previous time...) I found pretty much all my files. However, I go to the start menu, and under programs, there is no Accessories folder so to get an elevated cmd prompt, I have to type in cmd then push Shift+Ctrl+Enter. A window keeps popping up saying something about Catalyst not working. There was no link to the internet. (I had to go to the Network and Sharing center and click on "Internet" to download Firefox to post this) Also if I go to programs and click on the "Skype" folder (for example) it opens and is empty...How do I get my stuff back?

(Info if needed)
I was using Windows 7 64-bit (I think it was removed, but I doubt it, I'm not an expert at all)

Sounds like your system is FUBAR. Might be time to save your personal files, Wipe the Drive and reinstall everything.

If you do that try to be a little more discrete about where you go on the net, what you download from the net and how you deal with emails from sources you do not know.

Good Luck and Best Wishes.