Transfer soaked navy beans and soaking water to a saucepan. Bring to a boil. Reduce heat and simmer until nearly tender, approximately 1 to 2 hours. Drain and reserve the cooking liquid. Preheat the oven to 325 degrees F (165 degrees C). Arrange 1/2 of the beans in the bottom of a 2-quart casserole dish. Place 1/2 of the bacon strips over the beans and sprinkle 1/2 of the onions over top. Repeat layers once more. Combine ketchup, molasses, brown sugar, Worcestershire sauce, salt, pepper, and dry mustard in a large saucepan over medium heat; bring to a boil.
Pour sauce over the beans. Pour in just enough reserved cooking liquid to cover the beans. Cover the casserole dish with a lid or aluminum foil.
Bake in the preheated oven for 1 1/2 hours. Remove the lid and continue to cook, checking every 1/2 hour or so and adding more cooking liquid if necessary to prevent the beans from getting too dry, until beans are soft and tender, 1 1/2 to 2 1/2 more hours.
