1996 4runner alarm wont reset after flat battery

Question edited for clarity, full maker name.
Question moved to category, albeit '2005'.

Yes, it the battery goes flat, or is disconnected, the anti-theft and alarm needs to be reset.

https://www.google.com/search?q=2003+sl500+reset+security+system

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Battery went dead or replaced, it set the alarm. Some alarms can be reset with the key, some with a scanner, some at the dealer. Year, make , and model would be helpful.

battery may be flat in the fob or the vehicle has forgotten the code for the fob. and will need resetting. change the battery use the key to open the door put key in the ignition. ( fob Ir old type leave fob off the key) turn to number 2 and press fob till doors lock and unlock. then its reset. dont be worried if the alarm goes off while doing this it will go off when the code is restored. if you have 2 fobs you will need to rest that one to.

for security reasons this is difficult to reset usually the car and remotes need to be set up again. it happens when the car loses power so if the car is stolen or imobilised the car forgets the key codes.
take the car to a dealer or Machanic shop. prove to them it is your car and they will set the remotes back up for you.

i hope this was useful

engine management should read the transponder chip in your key and deactivate the alarm the battery in the key is charged while key is in ignition if the key hasn't been used for a while maybe its flat

There is more than likely a sequence to resetting the alarm, is the batterys in the remote flat as they are only 3 volts a piece (6 volts).

pull the fuse

stick key in drivers lock and un lock twice

try checking the fuses for the swithes themselves, usually under the dash or beside the doors

If it just clicks then i would suspect the battery is dead. Try to jump the battery.