2004 Malibu battery drain

My parents have a 2004 Malibu, my dad was sitting in the car last night, sick, while my mom went in to get medicine at Pharmacy, dad was opening the door, and tried to start the car to get heat, not sure what else he did, but when they tried to start the car, the battery was completly dead, trunk wouldn't shut, doors wouldn't lock. My brother jumped the car and they drove it home. Car starts but now there is a flashing lock and key signal on the dash that won't go away. What do we need to do, and will the car continue to start and run?