1996 4 Runner ignition theft deterrent

Okay let the laughing begin. I just bought a 1996 4Runner from my friend. Lots of rust, never really taken care of, a perfect project car. He is showing me all the ins and outs of his truck. To start it I have to hold this fob next to the panel neat your right knee, after hearing a beep, bingo you are free to start. He tells me it is an aftermarket part. Anyway to make a long story short, starting the truck this way is a real pain. He also tells me that all I need to do to eliminate this first step is to just get rid of that part. So I do...I find it and CUT the wire, and yep you guessed it it will not start, even after I rejoined the wire. Help.

Bring it either to a shop that specializes in alarms, or the dealer and have them troubleshoot it.

Well the ignition is fixed and all is good. Thanks for the advice. It took a little longer than anticipated, but managed to track down all the right wires and hooked them up and it has been perfect since.