The dealership installed an aftermarket alarm system in my VX when I bought it in 1999, but the factory installed system was left intact. In other words, when my remotes started failing (baby boy kept getting ahold of them... baby spit really does a number on electronics for those that didn't know) I just disarmed my aftermarket system and started using the stock remotes.
I don't know if the plug goes to the stock alarm, but I can tell you that mine is still plugged in.
Calmini Cone Air Filter, PowerVault PV2 Muffler, OME Trooper Springs, Rancho RS9000X Shocks, 285/75R16 Nitto Grappler AT's, Pioneer DEH P8000R In-Dash CD, Amps and Drivers Built by Orion, Wires and Fuse Blocks by KnuKonceptz, Vibration Damping by BQuiet, Alarm System featuring Auto Start and Remote Windows, Yakima LoadWarrior w/Full Size Spare, Debadged/Custom Titanium Grill Logo, Tint (5% Rear / 20% Front), Steel Braided Brake Lines, G2 Painted Calipers