Preheat oven to 375 degrees F.
Soak Navy beans in water overnight.
Drain and rinse beans.
In a large pot, combine beans, brown sugar, molasses, bacon, and onion.
Bring to a boil over medium heat, stirring frequently.
Reduce heat and simmer for 2 hours.
Season with salt and pepper to taste.
Pour beans into a 9x13 inch baking dish.
Bake for 30 minutes, or until heated through.
Serve and enjoy!