I have a 2004 Sonata where the key fob is worn so I used the key to enter the car. The alarm went off and I put the key in the ignition. Eventually I had to use my other key fob to shut off the alarm. Now the car won't start. I tried everything including disconnecting the battery for a while but the car would not turn over. I had to call a tow truck. When the dealearship tried it in the morning it started rght up. I'm concerned this will happen again. Any thoughts.

Sounds like a fault in the alarm system; it's not recognizing your key, which causes the alarm to go off and prevents the vehicle from starting. It could also be a problem with the key itself. If it happens again, try relocking the doors and opening it with the FOB that works.

I just had this same issue with a 2003 Hyundai Sonata and called a Hyundai Dealership. Get into the car on the drivers side, put the key in as if to turn it on, making sure the radio comes on (to ensure its not the battery). When all the lights come on, roll down the drivers side window all the way and let the alarm cycle two times. Then take the key out and wait for about 60 seconds. The car should start. I can't believe it worked, but it did.