Fan won't stop spinning, windows going up and down???
 

I finally got my trunk open, but there's something seriously wrong with my 2001 Boxster S. The fan won't stop spinning and it drained the battery, so I connected jumper cables and when I try to start the car, the lights on the dash flicker and the windows keep twitching up and down.... Maybe this video will explain it better.

https://www.youtube.com/watch?v=bir2xWvFlD4&feature=youtu.be

Check the immobilizer under the drivers seat for water damage.

Next suspect would be the ignition switch !

Definitely a prime suspect!

A weak battery can cause all kinds of strange behavior. Check the carpet under the driver seat for water
If dry, then replace the battery. If problem persists, then replace the ignition switch.

I have removed the immobilizer and it looks spotless. Is there anyway to test it?

Not really. If it looks good, move on.
Go to your local auto parts store to have your charging system tested. They should also have an ignition switch.