Well does anyone know how I can fix it? I wished I had never upgraded from Mavericks Sierra has been nothing trouble.
And I just noticed Desktop is missing in the Finder.
So, the order of the commands I listed is important. You ran cd Desktop and ls on two different sessions, which means you didn't get the expected output. Please open a Terminal window, and without quitting it, run the commands again:
"cd Desktop
ls -a"
or as someone else said, just do "ls -a Desktop"
Without knowing if the files are hidden or gone, we cannot help. Sierra moves the Desktop folder to iCloud if you so want it, and that's why you won't find it where you're used to in the User account in the Finder, but it still exists. As per your previous Terminal output, your desktop absolutely still exists, however, instead of asking Terminal what's in your desktop folder, you asked what's "above it".