Go to your local locksmith. Most have the "box" to program a remote. I paid 20 bucks for 1 remote.
Dealership
You have to program it with a DRB (Scan tool).
I had the same problem. Google "keyless entry remote 2003 Jeep Grand Cherokee".
dealer has to do it with factory scan tool
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.
Remote start was not available on a 1999 Jeep.
The only way to program keyless entry is with a very expensive diagnostic tool called "Launch" or go to nearest dealer for programming.
how do you program your remote
How do i program my remote car starter / lawless remote
The dealers scan tool is required.
It is easy to do with online instructions. Just google "2004 Jeep remote programming"
You can just contact your local jeep dealership and they can get you a new one and program it for you. I belive that the actual remote is usually around $30 and it doesnt take that long to program so the labor shouldn't cost to much depending on the hourly rate.