Heat the olive oil in a large pan over medium heat. Add the chopped onion and optional jalapeno pepper, sauté for about 5 minutes until softened.
Add the chopped garlic and stir for about 30 seconds to 1 minute until fragrant.
Season the chicken thighs with salt and pepper, add to the pan, and cook for about 2 minutes on each side to brown.
Blend the tomato sauce and half of the chipotles in a food processor until smooth, then pour over the chicken in the pan.
Stir in the chili powder, Mexican oregano, cumin, and adjust seasoning with salt and pepper.
Bring to a boil, then reduce heat and simmer for about 30 minutes until chicken is tender.
Remove the chicken, shred it with forks, return to the pan, and simmer for another 5 minutes.