Cobra car alarm not working?

I am able to operate the central locking and immobiliser with the door key but the fob will not operate anything.therefore i cannot set the alarm with the fob. i have had to disconnect three plugs in the front dash and pull out the plug on the siren to stop the alarm going off and the hazards flashing.i have tried resetting the fob but it will still not operate the central locking , alarm . any ideas? i think the whole problem could have been caused by a flat car battery.thanks but fob battery is brand new
Answer
I suspect the alarm has lost its memory, if the remote is a black tear drop shape with 2 grey buttons i may be able to help, you also should have a overide pen probe?? mail me if you want.