If this is the theft system that does not have the black puck in the key, then there is no way of disarming the sucurity system, but I understand some aftermarket alarm system bybass or work in tandam with the factory system, which involves reprogramming or auto learn of a new code, but does not disable or disarm the system. If you are having trouble starting and the car cranks and will not start or starts and dies, and the SECURITY light flashes then try this- Make sure you have a good battery this takes a toll on an old battery because the key will have to be left on for at least 30 min. With trans in park set parking brake, this turns off auto daytime driving lights, momentarily turn ign to start position( do not start engine) but then leave in run position without turning back to off. The security lightwill flash for a few seconds then stay on for 10 min. after the 10 min. and the light turns off, turn the ign. sw. to OFF for 5 sec. then repeat this prossess 2 more times. If your battery is weak and cant go through this prossess than it needs to be replaced. if this dosnt fix your problem you may need lock cyl, BCM, or Passlock sensor.
Hope This Helps