Soak beans overnight in cold water. Drain.
Simmer the beans in new water until tender, approximately 1 to 1.5 hours. Drain.
Preheat oven to 325F.
Arrange the beans in a large casserole dish, placing a portion of the beans in the bottom of dish, and layering them with bacon and onion.
In a saucepan, combine molasses, salt, pepper, dry mustard, ketchup, worcestershire sauce, and brown sugar. Bring the mixture to a boil and pour over beans. Pour in just enough water to cover the beans. Cover the dish with a lid or aluminum foil.
Bake 4 to 5 hours, until beans are tender. Remove the lid about halfway through cooking, adding more water if necessary to prevent the beans from getting too dry.