IF it is the alarm system, your battery will eventually drain and you'll hear a clicking sound (but lights will be flashing).
Try unlocking the lift gate or passenger door and then try to start your Jeep. If it starts right up and stays running, the problem was an "immobilizer" that cuts off your fuel pump when the car thinks it's being tampered with.
Good luck with a permanant fix as this is apparently a uniquely Jeep problem.
To permanantly disarm the alarm, here's another FixYa post:
I had the same problem with my '94 laredo just a few days ago. Seems this is a serious problem with jeeps. Here's how to fix it yourself. First, find the kick panel on the drivers side near the hood release latch. Remove the panel(2 screws). You will see a couple of bundles of wires...I know...I know...be paitent...you can do this...I did. Look for a purple wire with a yellow stripe. You will see other purple wires, but it HAS to be the one with the yellow stripe. It should be leading into a black connection. Trust me it's there. Once you've found the purple wire with the yellow stripe, the hard part is over. Strip a section of the covering to expose part of the wire. Do not cut wire in half. Then take a piece of similar gauge wire...I used speaker wire pulled in half...and connect one end of it to the exposed part of the purple and yellow wire. Take the other end of the speaker wire, and ground it to the metal part of your jeep with a screw. I ran my wire underneath the plastic trim leading from the kick panel down along floorboard and door opening. there are a couple of screws that hold the trim and carpet to the metal chassie. Wrap end of wire onto end of one of the screws and ground it to metal part of chassie. Adding a small washer will give it a more secure ground. Once you do these steps, your factory alarm will be disabled.
If it turns over and starts for a second or two then dies, its a either a computer problem or a bad crank position sensor
The power supplied to the fuel pump, ignition coil, fuel injectors,
and parts of the power module is controlled by the logic module through
the Automatic Shutdown Relay (ASD); the idea is to shut off fuel
pressure and the ignition systems when the key is turned off to prevent
fires, dieseling, and other problems.
The ASD relay is closed (allowing power to flow through
it) when the ignition is first turned on. If the signal from the
ignition reference is lost while the engine is running, or if the turbo
boost pressure reaches and exceeds the over boost cut-off point, the
logic module cuts power to the ASD, which in turn removes power from the
fuel pump, ignition coil, injectors and those parts of the power
module. This causes the engine to shut down.
Failure of the automatic shutdown relay is often shown as inexplicable stalling or refusal to start.
I’m happy to help further over the phone at https://www.6ya.com/expert/jeremy_69f3cc28d95bf514
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