I can think of 2 possibilities here - one is that the fuel tank and system cleaning, and new fuel will take care of the problem - the other is more serious, depending on what's actually in that fuel, damage to the CP3 pump and injectors may have occured. In either case, I would have a good Jeep/Dodge dealer with diesel mechanics do the repair, as you will need very good documentation from them if the pump and or injectors are damaged. Chances are that they're fine, but I would proceed as if they were negatively affected and have it thoroughly checked out and fully documented on your service record.
Suggestions on the vehicle:
Have it towed (don't run the engine) to a dealer and ask them to:
Drain and clean the fuel tank and lines
Replace the fuel filter, and keep a spare filter on board the vehicle just in case
Drain and purge the fuel rail, injector lines and return lines with a good diesel purge product
Add diesel fuel conditioner to the tank
Check the injectors for proper flow rate with their scantool diagnostic and other checks designated by the FSM
Check the fuel rail pressure readings to be sure the CP3 pump hasn't been damaged by that nasty looking fuel
If it isn't running correctly after that, have the injectors removed and tested.
Keep a sample of that fuel and receipt for proof of payment
Document all of the charges and present them to Shell as quickly as you can - it could be several hundred dollars or more if they have to remove the injectors and test them as well as clean the fuel tank. If the pump or injectors are damaged, replacement cost could be in the thousands
If any fuel pressure readings or injectors are off spec, ask Shell to pay for replacing the pump and injectors if necessary. You will probably need excellent documentation from the dealership showing off spec readings on the fuel pump and or injectors before this would be necessary or approved by Shell. It's critical to keep a sample of that fuel for lab analysis if Shell asks for proof before paying for anything more than fuel tank cleaning and replacement.
Let us know how it works out. There is at least one member here who had a bad fuel experience - iirc, his was a case of cleaning, not equipment replacement. Wouldn't hurt to ask him if I could remember who it was

Don't remember if it was OldNavy or not.