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How most immobilizers work? Your car keeps a database of allowed keys in the ECU. If it detects a key in the database, you can start the car. If it detects a key not in the database, it does not start.

Example 1: Your cars database has Key A, B, and C stored as allowed. You buy a new key K. When you put key K into your car, it sees K is not in the database and thus does not start. You need to program the cars ECU to allow Key A, B, C, and K.

Example 2: Your cars database has Key A, B, and C stored as allowed. You buy a new key N. You clone key N to contain the same data as key A. Now you essentially have two key A. When you put the new key into your car, it sees A and starts. You never had to touch the cars ECU because it already allows key A.

Technical Aside: Most keys with immobilizers utilize passive RFID technology. Essentially, the RFID reader (your car) sends out an electromagnetic pulse. The passive RFID chip (your key) has an antenna that uses this pulse to power itself. It then modifies the pulse to send its information back to the reader. This means that there is no battery in your key to power the chip.

CK-100 programmer. Attaches to your OBD-2 port and powers via standard 110V outlet.

Vehicle Model: 2004 Honda S2000

Situation: Got the used car which has only 1 key.

Device to program: CK100 (CK-100+) key programmer

For the S2000, the CK-100 erases all the keys stored in your ECU and then adds in all the ones you want. You must have all keys present when you use it. There are other programmers (Honda dealer) that can just add 1 key without having to erase all the keys in the ECU, but the CK-100 is not one of them (for S2000 anyways).

How to Program 2004 Honda S2000 Key with CK100 Key Programmer step by step

This is the SW version on my unit. v99.99 is the most current version as of Feb 2017.

Choose Immobilizer from the first menu to program your keys to the ECU

Choose Honda USA

Select your year S2000, I chose 03-05 since I have an 04

The CK-100 operates on a token system. Basically, you can use the CK-100 till you run out of tokens. Each task you perform with the unit costs a certain amount of tokens. After that, you need to buy a new CK-100 chip for new tokens. A new CK-100 comes with 1024 tokens. I think this screen is saying that it will cost me 8 tokens to program the S2000 ECU. However, it actually only used 1 as youll see later. Ive read that it cost 8 tokens each key for a Ford Explorer so it definitely varies by vehicle.

Not sure if you need an existing working key for this but I would assume so. I used my existing working key.

I chose to see how many keys were in my ECU before I erased it.

3 keys in the ECU, yet I only have 1 of them.

Choose Erase All Keys to start the process

Select Yes to confirm

Enter the number of keys you want to program into your ECU

I entered 2 since I only have 2 keys on hand

From here on just follow the steps as you see on screen. I might have missed a couple of off/on steps here (following steps and photographing is too difficult for me I suppose, lol)
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Here you need to look at your dash and see if the green key light is blinking or not. If it is blinking, it didnt finish correctly. Mine did not finish correctly the first time. I think I was too slow since I was taking photos. If the green key does not show at all, you are good to go.

Notice green key at bottom. (this photo was taken a day later to show the green key icon)

No green icon. Success!

If the procedure did not complete (Green key icon blinks), select No. You have 3 tries before it consumes your token. Select Yes once your are successful.

Only took 1 token from me to perform this procedure.

Here is a bug I believe. If you select yes, you can put in customer info (Last name, First name, vehicle info). However, after putting that info in, I couldnt exit the screen. I was stuck. I unplugged the CK-100. After I did that, only the first key I programmed worked. I then started over again and selected No the second time around. 1 more token used.

And thats it. I now have 2 working keys and a programmer to use on other cars in the future if I need it. Sure it cost more than the $50 at my local locksmith/dealer but it was more fun to do it myself. Assuming you use 1 token each time and pay $100 for the CK-100, this ends up costing you 9.8 cents each S2000 you program.