The factory Honda and Acura ECU's that are compatible with KTuner systems all have a built-in immobilizer system from the factory. The immobilizer system consists of the immobilizer equipped ECU, an immobilizer control unit under the dash, an immobilizer ring around the ignition slot, and a programmed key.
The KTuner software allows the immobilizer to be disabled from within the ECU. Disabling the immobilizer may be needed if you are installing a new or replacement ECU with KTuner and do not want to reprogram your keys/immobilizer for the new ECU, or if your immobilizer system is faulty. After disabling the immobilizer within the KTuner programmed ECU, the immobilizer control unit under the dash will detect a problem and flash the green "key" light on the dash indicating an immobilizer problem. To get rid of the annoying flashing "green key light" on your dash, simply unplug the immobilizer control unit under the dash and you are all set.
As a second option, if you are installing a new or replacement KTuner equipped ECU and you want the immobilizer to still work like factory, you can have your keys/immobilizer reprogrammed for the new ECU at your local Honda or Acura dealer. If you choose to go this route you must first flash the ECU back to stock and "unlock" the KTuner system from your ECU. Your Honda/Acura dealer can then reprogram the immobilizer system so that the car runs on your new ECU with your original keys. Once done, you can then lock the KTuner system back to your ECU and flash the ECU. Failure to unlock the KTuner system from the ECU first will cause the VIN in the ECU to change and your KTuner system will no longer be usable.