How to Make It
Combine beans and water to cover by 2 inches in a large bowl. Cover and let soak at room temperature 8 hours or overnight. Drain and rinse beans; set aside.
Cook bacon in a medium skillet over medium until crispy, about 10 minutes. Pour bacon and drippings into a 6-quart slow cooker. Add 2 cups water to skillet, and scrape up browned bits from bottom. Pour into slow cooker. Add drained beans, garlic, chopped chipotle, broth, salt, and 1 1/2 cups of the chopped onion; stir to combine. Cover and cook on LOW until beans are tender, about 6 hours.
Stir in lime juice, oregano, and cumin. Serve over hot cooked rice. Garnish with remaining 1/2 cup chopped onion and oregano leaves.