How do you reset the factory ignition security system after it has been tripped?

Resetting the Passlock system should fix it. If it doesn't you need an auto electrician or an auto locksmith.

https://www.google.com/search?q=2001+gmc+yukon+security+system+reset

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this year model did not come from the factory with a security system but many were installed at the dealer, is there a button under the steering column? if so i recommend you delete the alarm, if you ever have issues with the battery this will happen again. follow the wiring from the red light to the alarm control module and unplug the main clear connetor from the unit, also at the ignition switch you would have to unplug the ignition switch connector from the wire lead that goes to the alarm and reconnect the trucks factory connector to the igniton switch to take the ignition out of the alarm circuit

You can try this re-learn procedure, if that doesn't work you will need to bypass the security system. I hope you bought the wire harness adapter for that vehicle. They need it.

Perform the re-learning procedure

1. Turn ON the ignition, with the engine OFF.
2. Attempt to start the engine, then release the key to ON (vehicle will not start).
3. Observe the SECURITY light, after approximately 10 minutes the light will turn OFF.
4. Turn OFF the ignition, and wait 10 seconds.
5. Repeat steps 1 through 4 two more times for a total of 3 cycles/30 minutes
6. The vehicle is now ready to relearn the Sensor Data Code and/or passwords on the next ignition switch transition from OFF to CRANK.
7. Start the engine (the vehicle has now learned the Sensor Data Code and/or password).

Here is a link you can follow to learn more on the security system
http://diy-gm-security.com/ Do It Yourself GM Security bypass

I had this happen with a different vehicle. "My" issue was the security system. When I disconnected the wires going into the doors, it tripped the security system into the ignition lockout mode. I had to reset the computer (free and it only takes a few minutes). Mine was able to be reset with one of the code readers from O'Reilly Auto Parts which they will let you use for free. Some vehicles have a reset button built in. If you have a security system on your VW, first make sure all wires were reconnected and not broken during the installation of the doors. If everything checks out ok, then give your local VW dealer a call and ask to speak to someone in the service department. As the service person if there is a security system reset button anywhere on your car.

You need to reset the alarm system.That can be done with the remote entry key fob or by locking then unlocking the drivers door with the ignition key with all doors closed.This is for a factory alarm system.Also check the inertia switch,should be in the trunk,on the side with a push button top.Push button.If already down its not tripped.

If the vehicle has a 'Factory' alarm system, try cycling the jkey in the ignition ON-OFF (not to start), 5 times. This will defeat the factory alarm. This method is used in case the remote trasmitter battery goes dead, or the transmitter is lost.

This only works on Toyota Factory security systems, however.

you tripped the factory ignition security system . you may have a reset button near the fusepanel

You didn't say whether this was a factory or an aftermarket security system. Factory systems can usually be reset by using the key in the driver's side door, and turning key to "lock" then "unlock". An aftermarket system may benefit from having the ignition key in the "ON" or "RUN" position.

Sounds like your Passlock security system went into the tamper mode. If your dashboard security light blinks when the ignition is turned on, your Passlock security system is disabling the injector module, preventing the car from start. Try this:
1- turn the ignition on and just touch the starter, without getting the motor to fire, then leave the ignition in the "on" position. The security light will blink for about 10 minutes. When the light stops blinking, turn the ignition off and leave off for 3 minutes.
2-repeat the step #1, 3 or 4 times. You will know that is fixed when you turn the ignition on and the security light does not blink, then the car will start. Make sure to stay inside the car when you're doing this, as opening the doors will trip the security tamper mode on again. Once the tamper mode is off, the car starts and opening the doors will not trip the Passlock tamper mode.