it looks like the other end is plugged into some silver box. whats on that end?
Looks like that wire is a cut Apple Device connection wire. On the pioneer box it says "to iPod" which I can only guess it had a 30 pin connection on the other end that fits Apple devices. The stereo probably used the box as an adapter to use an ipod or iphone.
Edit: Damnit downpour you beat me to it....
hmm, I know for a fact there is one plug that ends up with nothing in it. I can't remember which on it is. Try moving the one from the hazards to the one for the clock and see if both still work. I know one plug fits in 2 places but only one place needs a plug in it, just don't remember which one.
Search the forum for "clock quit working"
This link might help, worth lookin at at least:
http://www.toyota-4runner.org/3rd-gen-t4rs/67728-i-found-problem-my-99-clock.html