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To reset the anti-theft system in a 2003 Ford Escape, you can do so using the door lock of your Ford. Put the key in the driver's side door lock and turn it without turning it back. Maintain this position for 40-60 seconds to signal to the system that you have the correct key. Repeat this process by turning the key in the opposite direction and holding it. Afterwards, remove the key from the door and put it in the ignition to start the engine. The anti-theft system is designed to prevent the engine from starting if it detects someone trying to use an unauthorized key or unconventional method.
Disconnect the positive cable from the battery, insert the key into the car and turn it to the on position, then reconnect the positive cable. Turn the key off and then back on; this should reset it. If the issue persists, you may need to visit a dealer to have the anti-theft system reset for you.