Lucivarious

I had an issue with my ignition switch being stuck in the on position. My car wouldn't shut off. I pulled the connector out of the distributer to kill the engine but because the ignition switch was stuck in the on position it still had juice going to it. That in turn fried the battery. I replaced the battery when the engine wouldn't crank but still no luck and now the immobilizer light on the dash is flashing green. The engine cranks but wont fire. I checked the spark plugs, the distributer cap for cracks, the coil for ware and everything is good on that end. I assume the ignition switch is still bad of course but i feel that the engine wont catch based on some security feature of some sort. My clicker wont unlock the doors or pop the trunk unless I pull the ten amp security fuse underneath the driver side dash. If i do that however the ignition, starter, engine wont get any juice at all. I got my immobilizer break code from the dealership and tried to enter that but it did not start the car. I was hoping for some input on how to override the ignition or the security feature so that i can start the engine at least. In my opinion if its just a bad ignition switch stuck in the open position, it shouldn't prevent the engine from starting. If anyone has encountered this problem before or know what to do please give me your advice on how to resolve the problem. Thanks!