Add bacon to a large Dutch oven over medium heat and cook until fat is rendered and bacon has begun to crisp.
Add onions, garlic, and red pepper flakes and saute until tender, about 4 minutes. Stir in the beans, tomatoes, brown sugar, thyme leaves, beef, maple syrup, apple cider vinegar, Dijon mustard, hot sauce, salt, and pepper and bring to a simmer.
Remove from the stovetop and bake uncovered 45 minutes until the mixture begins to bubble and thicken. Check at 30 minutes and add 1/2 cup water or chicken broth if it looks like it getting too dry.