You may have to do a little research but you can salvage the problem you may just be without your car until you can get it all sorted out. Since you have a spare key although it doesn't start the car at least you can get new keys cut from it so that's a start. There are two transponder types in the key fobs for the IS one is a valeo and the other is a Denso. The Denso transponder chip came out in the earlier models. You will have to check the cut off date, a later transponder (valeo) cannot be programmed to work in an earlier IS and visa versa.
You can pick the transponders up from eBay, there is a guy selling new keys with transponders for about £60-70 or you can do what I did and find an auction of a preowned key, get the transponder and transplant it in to a blank (making sure, as already stated, you check the length of your spare key the blade should be either 37 or 42mm)
One thing to note about the keys, (picture attached) you will notice on the right the Master has two grooves running down the side of it and the Valet key doesn’t. The grooves allow you to lock the Glovebox and open the boot which you cannot do with the valet key.
Once you have won you auction for a 3 button transponder chip and purchased a new 3 button case and got the key cut. Then you have to get your ECM flashed back to factory mode so you can program the new key on to your immobiliser. I hope the above points you in the right direction, there is plenty of info/advice on this forum. I was quoted £1700 by Lexus because I don’t have a master key, I've calculated by the time I get the ECM reflashed and keys programmed I will have saved myself about £1450 so it might be a bit tedious but will be well worth it!