Tender from-scratch navy beans in a sweet, smoky molasses and brown sugar sauce, baked low and slow in a covered Dutch oven, then finished uncovered until the sauce is dark and glossy.
Soak the beans. Rinse and sort the dried beans. Cover with plenty of water and soak overnight, about 8 to 18 hours. Drain and rinse.
Simmer the beans. Add the soaked beans to a large pot and cover with fresh water by about 2 inches. Bring to a simmer and cook 45 to 60 minutes, until the beans are starting to soften but are not fully tender. Drain into a jar or bowl to reserve the cooking liquid.
Cook the bacon and onion. Heat a skillet over medium heat. Cook the diced bacon until some of the fat has rendered but it is not fully crisp. Add the onion and cook 3 to 5 minutes, until softened.
Mix the beans. Heat the oven to 300°F. Add the drained beans, bacon, onion, molasses, brown sugar, Worcestershire, vinegar, salt, and pepper to a Dutch oven or covered baking dish. Add enough of the reserved cooking liquid to barely cover the beans and stir gently.
Bake covered. Cover and bake 3 to 4 hours, stirring about once an hour. If the beans look dry, add a splash of hot water.
Bake uncovered. Remove the lid and bake another 30 to 60 minutes, until the beans are very tender and the sauce is dark, glossy, and clings to the beans.
Rest. Let the beans rest 10 to 15 minutes before serving. The sauce will thicken a little more as it cools.
Notes
The beans should be very tender and creamy inside, but still mostly holding their shape. If the flavor tastes too strong after chilling, reheat the beans before judging. Cold baked beans can taste more intense, because the sweetness is muted and the molasses, bacon, and Worcestershire stand out more.Slow cooker option: After soaking and simmering, add everything to a slow cooker with just enough water to barely cover. Cook on LOW for 8 to 10 hours, until very tender. If the sauce is thin, cook uncovered on HIGH for 30 to 90 minutes, or transfer to a baking dish and bake uncovered at 350°F for 30 minutes.