Factory security system
I had an aftermarket alarm on a Wrangler and encountered the same problem. With the car off I disconnected the battery, then pulled the fuse(s) for the alarm. I waited to reconnect the battery for about 10 minutes because the computer can hold memory with no power source for a short amount of time. (I did not put the alarm fuses back in.) This disables the alarm, but atleast the Jeep started.
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