*WARNING* doing this prank to a very grumpy or angry person may result in very painful consequences. Do at your own risk!
Step 1: The Setup
1) Alarm Clock
That's it!!! nothing else.
So to start this prank all you need to do is when your target (friend) is no where to be seen all you do is sneak into their room. Make sure you give yourself a good time allotment so you are not caught. Once in the room you need to set their clock ahead about 30 minutes or so. That way in the middle of the night their alarm clock will go off making them think they are late for school or work.