Thankfully, this horrible glitch only works on the Wii. It's simple to do, and will make your file start over.
After accessing the room under Kakariko with the cannon, Save and quit. You should appear in the room after you come back, but Shad won't be there, and there's absolutely no possible way to get out, since Midna thinks Shad's still there, but he isn't, and if you try to leave, Shad, who is all the way through the wall, will tell you to not leave. The only way out is to restart the file.
Submitted by: Dremo