Found this online, this worked on my wife's 2000 Protege:
Step 1: Open drivers door and leave open.
Step 2: Lock and unlock the drivers door using the power door lock switch on the door.
Step 3: Insert key into the ignition.
Step 4: Turn key to on position and return to off position. (IMPORTANT - use ON position NOT ACC position). Do this 3 times within 10 seconds. Leave key in the ignition.
Step 5: Close and open the drivers door 3 times. (Door should be left open after this step).
Step 6: ECU should respond by locking and unlocking the doors.
Step 7: Press any button on remote #1 2x. ECU responds by locking and unlocking the car doors.
Step 8: Press any button on remote #2 2x (etc.) Each time the ECU will respond by locking & unlocking the doors.
Step 9: Remove the key from the ignition and the ECU will respond a final time with a series of door locks and unlocks. You're done!
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