Q: I took out my aftermarket anti theft system how can I reprogram it to be able to start my 2003 ford Explorer

If the check engine light is on, the diagnostic starts there, that is the Trouble Codes have to be downloaded and interpreted, especially in your circumstance as it is not clear from your inquiry that the no start is related to the immobilizer or is perhaps due to some other fault. A bottom line is if you request a no start diagnostic the responding certified mechanic will certainly pin it down one way or another. The Explorer uses a passive anti-theft system (PATS). If the system has been triggered, the red warning light on the dash will flash much faster than normal and it will remain in this mode until either the proper key is inserted and turned in the ignition or 15 minutes has passed. To disarm PATS, you can insert a known correct key into the ignition and turn it. Note that if you use a non PATS key, such as one that was cut simply to open the doors from an all-metal key blank, the system will remain armed. If the Explorer starts, then you have disarmed the PATS system. If the vehicle doesn’t start, verify that you have the right key. A Ford PATS keys has a large black plastic, or molded rubber, head. Inside the head is a transponder chip that is programmed to a certain code so that the PATS transponder in the vehicle recognizes the key. It is possible for a PATS key to lose its programming, but highly unlikely. If you are certain you have the correct key, try to start the car with a spare known good PATS key. If the car still won’t start, wait 15 minutes, until you see the flashing rate on the red light on your dashboard decrease to normal speed and then try both keys again. If this still fails to start the car, disconnect the vehicle battery for 15 minutes, then reconnect it and try again. If all those steps are unsuccessful, request a no start diagnostic and the responding certified mechanic will get this taken care of for you. If you have further questions or concerns, do not hesitate to re-contact YourMechanic as we are always here to help you.