97 Camry Anti-Theft System Problems - Help!

I have a 97 Camry with the Anti-Theft System. The remote is integrated with the key. Just replaced an old dead battery and alarm system seems to be acting up. Replaced battery in remote twice. The anti-theft system also has an engine immobilizer that prevents the car from starting. Is there a particular procedure I can use to reset the anti-theft system or bypass or disable it? The owners manual gives no help, but does mention that disconnecting and reconnecting the battery will set off the alarm. Seems like the remote does nothing to either stop the alarm from sounding. Could it be possible that 2 new batteries in the remote were both too weak? Thanks in advance Dave