1 pound dried navy or pea beans (about 2 1/2 cups)
8 ounces thick-cut bacon slices (about 6 slices), small dice
1 medium yellow onion, small dice
2 1/2 cups water, plus more for soaking the beans
1/2 cup ketchup
1/4 cup dark molasses, also known as robust (not blackstrap)
1/4 cup packed dark brown sugar
1 tablespoon cider vinegar
1 tablespoon Dijon mustard
1 tablespoon kosher salt, plus more as needed
1/2 teaspoon freshly ground black pepper, plus more as needed
1/8 teaspoon ground cloves
Place the beans in a large bowl and pick through them, discarding any broken beans or stones. Cover the beans with at least 3 inches of cold water. Allow to soak uncovered at room temperature for at least 8 hours or overnight. Drain in a colander and reserve the bowl (no need to wash); set the bowl aside. Place the beans, bacon, and onion in a slow cooker.
Whisk the remaining measured ingredients in the reserved bowl until combined. Pour into the slow cooker and stir until thoroughly combined. Cover and cook on either high or low heat until the beans are tender and the liquid thickens slightly (it will thicken more as it cools), about 6 hours. Taste and season with salt and pepper as needed.