Soak the dried navy beans in water overnight, ensuring they are covered by at least an inch of water.
Preheat your oven to 250ºF.
Place a cast-iron Dutch oven over medium heat.
Add chopped bacon and cook until the fat renders, about 5 minutes.
Add the diced onions and jalapeños, cooking until the onions are soft.
Mix in the tomato paste, dark brown sugar, and molasses.
Stir until the mixture is well combined and sugar is dissolved.
Drain the soaked beans, saving the soaking liquid for later use.
Add the drained beans to the Dutch oven.
In a measuring cup, combine the soaking liquid with 4 cups of vegetable broth.
Pour this mixture over the beans in the Dutch oven.
Add black pepper, cayenne pepper, and salt to taste.
Bring the entire mixture to a boil over high heat.
Once boiling, cover the Dutch oven and transfer it to the preheated oven.
Bake it for about 6-8 hours or until the beans are tender and the sauce has thickened.
Serve hot.