Sorry if this is answered somewhere but I tried searching here and on Google but there's not to many threads talking about the immobilizer since they were only in 98+ SC.

So I just made the switch over from my 02 Is300 to a 99 SC400 and the person I bought the car from had two keys. One was the "Master Key" with the key fob built right into the key and another key that looked like a generic cut key. The issue I am having is that the "Master Key" is not able to start to the car but it is programmed to unlock/lock it yet the generic one is. I'm assuming that the "Master Key" needs to have the immobilizer set/programmed? I have no idea if this is something I can do or if I would need to go to Lexus dealership to figure out but any input would be great.

 

Your remote is programmed but the key is not, when i got my master key cut, it was programmed to the vehicle after, along with the remote functions. You'll have to head to the dealership or find a locksmith that could do a ecu flash to program your key. The flashing my be a bit expensive, since they have to pull the ecu, but check with the dealer first.