1997 Honda Civic: Battery died and the Alarm won't disable

What year is this? Is this a factory OEM system?

have you renewed the remote key battery, they should be renewed every 2 yrs ?

Disconnect car battery for 10 minutes

Might have broken wiring harness wires that run from the cabin to the door. There is a rubber boot that covers this harness, runs near the door hinges, remove boot and check all wires and if you find any damaged or broken, repair and test auto door lock.

Usually when you change a Fob battery you have to re-sync it to the car. Some cars have you lock and unlock the drivers door with the key.
Should be in your owner's manual.

try disconnecting the battery neg lead and the pos lead then join them together for 5 mins then reconnect the battery and see what happens ,it might just reset the fault for you .

Here are the options for disarming a factory alarm while it's going off:

1. Close all doors, trunk and hood. Alarm will stop after preset time.

2. Hit the unlock or lock button on the remote. (One of the 2 works... I just don't remember which.)

3. With all doors, trunk and hood close, insert the key in the driver's door and unlock/lock the doors manually.

Also, is it a factory security system? Is it a honda key fob? or a remote start system perhaps?

check remote batt..if that dont work unhook car batt for 24 hrs. should reset

I had this happen today and called an alarm installer. he said to connect the battery cable (id unhooked it to stop the blaring) then open the door to set off the alarm. then torn on the key ( even tho it wont start the car , turn it on anyway) then look for a toggle switch ( AKA a valet switch) with the key in the on position flip the switch. ( when I did this a noticed a tiny red light come on to the left of the steering column) I turned the toggle back to the original position and then I tried to crank -AND IT CRANKED WITH NO SCREAMING ALARM!!! I was so happy, I had to post this in case it could help someone else.

All alarm issues aside, the radio losing its settings would make me go and clean the battery cables.