Preheat your oven to 300°F (150°C). Lightly grease a medium casserole dish.

In a large skillet over medium heat, cook the chopped bacon until crispy. Remove the bacon pieces with a slotted spoon and set aside, leaving the rendered fat in the skillet.

Add the chopped yellow onion to the skillet with the bacon fat and sauté until softened and translucent, about 5-7 minutes.

In a medium bowl, whisk together the brown sugar, molasses, ketchup, apple cider vinegar, dry mustard, smoked paprika, Worcestershire sauce, and water until the sugar is dissolved and the sauce is uniform.

In the prepared casserole dish, combine the rinsed navy beans, the cooked bacon (reserving a small amount for garnish, if desired), and the prepared sauce mixture. Stir gently until everything is well coated.

Bake uncovered for 3.5 to 4 hours, stirring gently every hour, until the sauce has thickened considerably and the beans are tender and caramelized on top.

Remove from the oven, let cool for 10 minutes before serving. Garnish with reserved bacon pieces.