My Spotlight, desktop items and shutdown/restart items have gone missing

I was playing Subnautica and then I quit after glitching out (unrelated to what has happened) and then all my folders/applcations went missing from my desktop. If I look in my desktop folder it still has everything there. I've tried that terminal command (defaults write com.apple.finder createdesktop -booltrue && killall finder) but it did not work. I looked for my spotlight and realised it wasn't there and then I looked at my dock and there was only finder and next to the bin was My Applications, Documents and Shared. Also when I looked at my Launchpad there was only one folder that I made. All my applications are still in Finder, but nothing nowhere else. Could someone please help me ASAP I need this fixed for my school project. (p.s. I have tried restarting several times and it has not changed a single thing besides the fact that my dock keeps restarting. An I can't do a normal shut down or restart).