Soak beans overnight in cold water. Simmer the beans in the same water until tender, approximately 1 to 2 hours. Drain and reserve the liquid.
Preheat oven to 325 degrees F (165 degrees C).
Arrange the beans in a 2 quart bean pot or casserole dish by 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 of the reserved bean water to cover the beans. Cover the dish with a lid or aluminum foil.
Bake for 3 to 4 hours in the preheated oven, until beans are tender. Remove the lid about halfway through cooking, and add more liquid if necessary to prevent the beans from getting too dry.