Place navy beans in a large bowl and cover with several inches cool water; let soak overnight.
Drain beans; place in 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; save bean-cooking liquid.
Preheat the oven to 300 degrees F (150 degrees C).
Place beans in a clean Dutch oven; add bacon, onion, molasses, brown sugar, dry mustard, salt, and black pepper. Pour in enough hot reserved bean-cooking liquid to cover beans; stir.
Cover Dutch oven; bake in the preheated oven 1 hour. Check liquid level; add more reserved bean-cooking liquid to cover beans. Return to oven; continue baking until beans tender and almost all liquid absorbed, about 1 hour.
Increase oven temperature to 350 degrees F (175 degrees C). Uncover beans; continue baking until top develops a flavorful crust, 20 to 30 minutes more.
