In a large Dutch oven, bring the oil up to medium heat. Add in the onions and sauté until golden brown, about 5 minutes. Next add in the garlic and cook for 2-3 minutes.
Add in the chicken thighs and season liberally with salt and pepper. Next add in the canned tomatoes, chipotles, chipotle sauce and chicken stock. Stir to combine, cover, reduce to simmer and cook for 2 ½ to 3 hours, stirring occasionally.
Remove the lid during the last hour of cooking so the liquid reduces into a thick sauce. Break up the larger pieces of chicken with the back of a wooden spoon or with 2 forks. Season with salt and pepper and finish with the lime juice.
Serve inside warm tortillas with cheese, lettuce, avocado and sour cream.
Recipe Adapted from Food & Wine.