Drain and rinse the soaked beans and set aside. Preheat the oven to 300 degrees F.
Add the chopped bacon to a large Dutch oven, and heat over medium high heat. Cook the bacon, stirring occasionally, until the fat has been released and the pieces of bacon have separated from each other, about 5 minutes. It will not be crisp.
Add the drained beans, molasses, brown sugar, and mustard to the pot. Stir to coat the beans.
Pour in the water and bring to a boil over high heat. Once boiling, add the onion and garlic and cover with a lid.
Transfer the beans to a 300 degree F oven and cook for 3 ½ to 4 hours until the beans are tender.
Remove the garlic clove and onion from the pot and discard.
Stir the mixture and let the beans sit for 30 minutes to cool and to allow the sauce to thicken.
Give the beans a taste and season with 1/2 teaspoon of salt and ground black pepper to taste.