Step 1: Soak the navy beans overnight in a large bowl of water. Ensure the water level is at least 3 inches above the beans. Drain and rinse the next morning.
Step 2: Place the soaked beans in a large pot with 6 cups of fresh water. Bring to a boil, then reduce heat and simmer for 45-60 minutes until the beans are tender but not mushy.
Step 3: Preheat your oven to 325°F (165°C).
Step 4: Drain the cooked beans, but reserve 1 cup of the cooking liquid.
Step 5: In a large oven-safe casserole dish or Dutch oven, combine the beans, diced onion, and minced garlic.
Step 6: In a separate small bowl, whisk together the molasses, tomato paste, apple cider vinegar, mustard powder, smoked paprika, liquid smoke, and black pepper.
Step 7: Pour the sauce mixture over the beans and stir well to coat. Add the reserved cooking liquid to ensure the beans stay moist during baking.
Step 8: Cover the dish with a lid or foil and bake for 2.5 to 3 hours. Check every hour; if the beans look dry, add a splash of water.
Step 9: Remove the lid for the last 30 minutes of baking to allow the sauce to thicken into a dark, smoky glaze.
Step 10: Let the beans rest for 10 minutes before serving to allow the flavors to fully settle.