The factory alarm won't shut off

if fine the fuse for the alarm, remove the fuse, see if it will start and then shut it off, than replace the fuse.

or

try just removing the negative off the battery post of the battery of the car that will reset everything in the car.

The alarm system somehow got activated , this is usually because the battery becomes discharged or disconnected try doing this:
Remove the key from the ignition
disconnect the negative battery terminal
put the key back in and turn to ON
exit the truck and leave door open
reconnect the battery terminal
get in and leave door open, if the alarm horn stays off it should start.

Disconnecting the car battery will reset the alarm system. When you first connect the car battery, the alarm will sound briefly, then stop. You will have to retrain the alarm system to recognize your remotes. The procedure for that varies from one year model to the other. On my 1998 you do it by putting the key in the door lock and holding it full counterclockwise until you hear a brief beep from the alarm horn. Then press a button on your remote and the system will learn to recognize that remote.

NO.to reset the factory immobiliser/alarm you must unlock/hold key over 30 secs....then lock/hold key over 30 secs....then press unlock button on remote for 30 secs....reset.(if you disconnect the battery you will have to reset AGAIN and input radio code.)

factory alarm, when manually unlocking the door the lights flash & horn usually go off & the car will start & shut off within a second or 2. Have 2 96 jeeps that do it the panic button on the keyless entry is the only way to shut it off. If the battery has died & a new one is installed it trips the panic mode as well. If the battery is dead but vehicle starts with a jump but shuts off soon after jumper cables are removed, the alternator is bad & cant keep the computer powered up & will shut down the vehicle. A little more specific with symptoms will make diagnosing much easier.

all doors hood and trunk must be closed and locked unlock drivers door with key alarm should stop (this will apply to factory alarms ). if you have an after market alarm you should use the control box. If battery is low or bad you must replace it before you can shut off the alarm

My 4Runner did the same thing. What I did was just put a new battery in hook it up and let it honk. Put the key in the ignition and start it and it should stop. It is in alarm mode.

When they install a alarm, there is a switch, usually under the dash, in the side by your feet, lot to far from teh fuses and the light. Depending on the alarm, it is a small flip switch you will be looking for, you just switch it off, and then it will beep, hit the remote and it should disable it, I had to call a alarm company for the exact sequance, but they will disengage

hope it helps

find the fuse for the alarm and pull it out tha=is should solve it, but means you have no alarm

your transmitter has posably a bad battery or the transmitter codes were erased when you took the battery terminals loose