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If the key fob stopped working then the first thing I would recommend is checking or replacing the battery. The battery may have died and it is now not transmitting when you press the button. If it still doesn't work or you find the battery voltage is ok then you can have the fob tested for free at most large parts stores like Autozone. If it isn't transmitting then it will need to be replaced.
The key not opening the door or trunk could be a couple things.
It's not uncommon for someone to have lock cylinders re keyed after losing keys or having them stolen. The ignition key could be correct for the car but the other lock cylinders have been changed.
The ignition lock cylinder may have also been changed and now uses a different key, leaving the original ones in the door and trunk. You can try having a locksmith or your dealer cut a key with the VIN and see if you can get in the door and trunk.
It could also be an issue with the door and trunk latches, the lock cylinder linkage to them, or the lock cylinders could have both failed.