I have a Scorpion Alarm on my E34 and one day I went to start the car and the battery had practically died.
The alarm decided to constantly sound when another charged battery was connected and I couldn't disarm it with the fob.
Spoke to an alarm specialist that happened to be walking distance from me and he suggested the following:
Put key in ignition
Turn ignition on (dashboard lights illuminated)
Press both keys (or one of them) for 5 seconds.
I had to push the buttons randomly, can't recall what I did exactly but it worked and the alarm responded and reset itself and stopped annoying the neighbours.