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What you describe sounds like a problem with the security key. It's possible that the chip in they key has dies and won't transmit the start signal to the security code receiver in the dash.
Do you have a spare key you could try?
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If it is the security key acting up then there is no way to bypass it. You might be best off calling a locksmith to see if they can come check the transponder (the part in the key) and the transceiver (the part in the dash). You could try changing the battery in the key fob, but it might not work.
A locksmith (a good automotive locksmith) should be able to check communication. If you can't find one, you might have to go to the dealer.
They will then determine if the key is faulty or the module in the dash needs replaced. After replacement they will reprogram the security system.
It's very common, but the only way to fix it is with the scan tool that can communicate with the security system.
If you would like instructions on how to replace the dash module yourself I can send over a diagram, but it will still need to be programmed before it will work.
Here is the procedure for replacing the dash module. Jeep refers to it as a SKREEM/WCM in this diagram.
The most likely cause is a bad key, so I would look into that first.
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I just wanted to see if you needed any additional help. I never received a response from you so I assume you got it sorted out. Please let me know if I can be of any assistance.