In a large microwave safe bowl, add the onions, red peppers, chili powder, vegetable oil, garlic cloves, cumin, and oregano. Microwave in 1 minute bursts for 5 minutes, until the onions are softened, stirring after every minute.
Add the broth and water to the slow cooker. Stir in the onions, beans, and sausage.
In a small bowl, whisk the soy sauce, brown sugar, minced chipotle, and liquid smoke. Stir into the slow cooker. Add the bay leaves and let cook on low for 9 to 11 hours.
Let the chili chill for 5 minutes off heat. Skim and needed fat from the surface. Strain 1 cup of cooked beans into a shallow dish and mash with a potato masher. Stir the mashed beans back into the chili and allow to thicken 5 minutes. Season with salt and pepper as needed.
Ladle into bowls and serve with scallions.