Soak navy beans overnight in a large bowl with enough water by several inches. Drain and place beans into a large Dutch oven or heavy pot with 6 cups water, baking soda, and bay leaf. Bring to a boil, reduce heat to medium, and boil for 10 minutes. Drain, saving bean-cooking liquid.
Preheat oven to 300 degrees F (150 degrees C).
Transfer beans into clean Dutch oven and stir bacon, onion, molasses, brown sugar, dry mustard, salt, and black pepper into beans. Pour enough of the hot reserved bean liquid in to cover beans; stir.
Cover Dutch oven and bake in preheated oven for 1 hour. Check liquid level and add more of the reserved bean liquid to bring liquid up to cover beans. Return to oven and continue baking until beans are tender and almost all the liquid has been absorbed, about 1 hour.
Raise oven heat to 350; bake beans uncovered in oven until top develops a flavorful crust, 20 to 30 more minutes.
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