I had a similar problem on my girlfriend's ST205 a couple of weeks ago, the positive battery terminal came loose and spiked the alarm. It was a Toyota 5000 alarm, standard fit thing that has an immobiliser and controls the central locking etc.
I spoke to my friendly Mr T parts guy who suggested the following, and suprisingly it worked:
1. Open the drivers door and leave it open just in case the alarm turns on and locks you out!
2. Turn the ignition on to ACC.
3. Disconnect the positive terminal of the battery for about 5 seconds and reconnect as cleanly as you can (without sparking etc.)
4. Turn the ignition off
5. Press the black button. The alarm should respond. If not, try holding the black button for 10 seconds as per Ratboy's instructions to re-sync the keyfob to the alarm unit.
This should sort it, the technician apparently said sometimes you have to repeat this 2-3 times before it will work, but if the alarm unit is still ok then this should sort it out.
When I reconnected the battery, before I even took the keys out of the ignition it had started flashing the hazard lights so the alarm had already started working again.