Sadly this is gonna require a visit to the dealer. Plan on spending $40 or so to get this done. Every Jeep from 1996 or so onward will need a dealer program to get keyless working.
It is easy to do with online instructions. Just google "2004 Jeep remote programming"
You might need to programming the remote. Their should be instructions in the users manual. You're remote could also be need new batteries.
I had the same problem. Google "keyless entry remote 2003 Jeep Grand Cherokee".
The only way to program keyless entry is with a very expensive diagnostic tool called "Launch" or go to nearest dealer for programming.
You have to program it with a DRB (Scan tool).
dealer has to do it with factory scan tool
Remote start was not available on a 1999 Jeep.
Above your rearview mirror there should be a small black 'ball' (extending from the roof of the car). That is your module. If it's not there, I'm not sure if your Jeep has it. You can always refer to the owner's manual (you can snag one from eBay cheap if you don't already have it) or drop by your Jeep dealership to have them find out for you. Hope this helps!
A programmed RKE fob (remote) or a chipped key is required.
You need a remote start system that works with the alarm/smart key system. You can not just unhook the alarm.
If you have 2 (a pair) it tells you in owners manual to program the 3rd. If you are programming a second, you will have to goto dealer so they can program it with drb3.