Drain and rinse the soaked navy beans. Place them in a Dutch oven and cover with fresh water. Bring to a boil, then reduce heat and simmer for about 1 hour until tender.

In a mixing bowl, combine ketchup, water, brown sugar, molasses, mustard powder, smoked paprika, salt, black pepper, chopped onion, and minced garlic. Mix well.

Preheat the oven to 300°F (150°C). Drain the beans and add them to the sauce mixture. Stir to combine, then transfer to a baking dish.

Cover the dish with foil and bake for 1 hour. Remove the foil and bake for an additional 30 minutes until the sauce is thick and bubbly.