To an oven-safe skillet with a lid such as a cast iron skillet or braiser, add the bacon. Par-cook over medium-high heat, 1-2 minutes per side, until golden & rendered slightly. (The bacon does not need to be crispy at this point – it will continue to cook in the oven with the baked beans). Remove from the skillet & carefully slice into 1-inch pieces. Set aside.
If using a variety of sausage that is not fully cooked, brown the sausage in the rendered bacon drippings. Place the chopped sausage in the skillet. Reduce heat to medium. Cook 4-5 minutes, stirring occasionally, until the sausage is rendered & browned. Remove from the skillet & transfer to a paper towel-lined plate to drain.
Carefully remove all but 1 Tbsp of the rendered bacon/sausage drippings from the skillet. Add the onions & season with a good pinch of kosher salt & ground black pepper as desired. Cook 4-5 minutes, stirring occasionally, until softened & fragrant.
Meanwhile, as the onion softens, whisk together the chicken broth, ketchup, brown sugar, molasses, Worcestershire sauce, yellow mustard, & red wine vinegar. Once the onion is softened, add the navy beans & sausage to the skillet. Pour the brown sugar mixture over top, stirring gently to combine well. Arrange the par-cooked bacon over top.
Cover the skillet & transfer to the oven. Bake 30 minutes, until the beans are warmed through & bubbling around the edge of the skillet. Carefully remove the lid & bake for an additional 15 minutes, or until the sauce is thickened to your desired consistency. Remove from the oven & allow to cool slightly.
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