How do you know if it the immobiliser? Does your anti-theft light flash constantly when you try to start it? Usually when the anti-theft has kicked in the engine won't even crank over. There is usually an antenna around the lock cylinder to detect the key and It may have been damaged. Other than that, there no way to bypass the system.
Had a similar problem where my escort wouldnt start. The immobiliser LED didnt light up when i tried to start the car nor did the starter turn over. Ford found the fault which was a dodgy wiring to the Power Hold relay. Check these things first before suspecting the immobiliser otherwise Ford will charge you nearly £200 just to fix a wire!!!
http://www.motor.com/MAGAZINE/Articles/042006_11.html
Electronic Junkie03, April 2007
