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If the remote was programmed before loss of power, push and hold the unlock button until the alarm stops. If not try locking and unlocking the drivers side door with the the key. This has reset the alarm on my 2001 Odyssey.
You will also need the unlock code to reactivate your stereo after long term power loss. It is on a card with the manual given to the owner of new vehicles. A smart dealer will put it on a sticker in the glove box. Otherwise you have to remove the radio and give a Honda dealer the radio serial number to get the unlock code. Don't try it randomly; 10 incorrect tries locks the stereo.
Sounds like a bad battery. If the battery is OK than lock and unlock your Toyota with your fob. If it is still dead than take the better terminal cables off and touch the negative and positive cables together while both are disconnected and away from battery terminals. Should reset your anti theft system. Connect the cables back and try to start. again. If no crank likely bad battery. If battery is OK but no crank then it is the starter.
You should have disconnected the battery and fully charged it before starting the car.
The low voltage may have damaged some of the electronic components in the alarm system.
Charge the battery fully, then reconnect it and see if that helps.
If this is an after market alarm, an alarm that was installed by someone other than a dealer there will be an in-line fuse under hood on the main power wire leading to the alarm horn. Usually along the firewall. Remove this fuse and you should be able to start the vehicle. The problem you are experiencing is the anti theft or ignition kill switch being activated because the alarm is detecting the lose of power as a Surge and triggering the anti theft circuit.
Some possible solutions that might help:
1. I'm not sure if this model comes with a Master Ignition key (which is usually a different colour fob or shape). If it does, then try starting the car with the Master key, it should override and reset the antitheft system and allow the car to start.
2. The Alarm keyfob (if it has one) battery may need replacing.
3. There may be an override key operated switch on the alarm itself or secreted away somewhere inside the car, which you can use to activate/deactivate the antitheft device?
4. You may have to key a code number onto a set of buttons on the dashboard to reset the Antitheft device?
5. Do you have the User Manual for the vehicle. There should be some explanation in there about what precautions to take when replacing the vehicle battery, and how to reset the anti theft device so that the engine can be started again