Fry bacon in a frying pan on medium high heat until crispy. Remove to paper towel and drain excess grease. When cool chop into bite-sized pieces.
Drain bacon grease, leaving two tablespoons in the pan. Saute the pepper and onions over medium heat in the grease until transluscent. Add minced garlic and saute another 1-2 minutes or until veggies are tender.
Drain the beans and place in the crockpot. Add the bacon, sauteed veggies, tomato sauce, molasses, apple cider vinegar, worchestershire sauce, brown sugar, yellow mustard, dried red chili pepper flakes (optional) and pepper and stir everything together to combine.
Cover and cook on high heat for 3 hours, stirring occasionally. You may taste the beans and adjust the seasoning as desired. Add more red chili pepper flakes if you want more heat. You can add a little water a tablespoon at a time if beans seem too thick.
After 3 hours turn the heat back to low until ready to serve.