You just need to turn the Unity plugin back on. The problem is this is a pain in the bottom because you've now got no graphical method to do this. So:
Try to open a terminal with Ctrl+Alt+T.
This may not work but you can try right clicking on the desktop and selecting "Open terminal here." Otherwise, you may need to change to a "hard" terminal by pressing Ctrl+Alt+F1 and log in.
Install compizconfig-settings-manager by running
sudo apt-get install compizconfig-settings-manager
Then run it with this:
DISPLAY=:0 ccsm &
The first part tells the terminal which display you want it to load on (otherwise it won't have a clue).
If you switched to a TTY in step 1, switch back to the graphical server by pressing Ctrl+Alt+F7 (or Ctrl+Alt+F8 sometimes).
There there should be a CompizConfig Settings Manager waiting for you.
Find the Unity plugin. Enable it. You will be asked "Ubuntu Unity Plugin requires the plugin OpenGL. Enable Ubuntu Unity Plugin / Enable OpenGL"
Everything should spring into life but if it doesn't, you might have to restart. You can do that by going back to the terminal and running sudo reboot.