The 'other end' is simply the cable from the alarm unit. You can leave it as, tie it out of the way, tape over it and tie it up, or remove the alarm unit and put it on a shelf. The dash display will still show 'CODE' at start up, but just ignore it. As for why did I remove mine...I didn't trust the little blue arm/disarm transponder, and use locks if I am securing my bike.
Stephen