
Heat the oil in a large pan to medium heat and add the onions and jalapeno peppers. Cook them down about 5 minutes.
Stir in the garlic and cook for 30 seconds to 1 minute, until the garlic becomes fragrant.
Season the chicken thighs with salt and pepper, then add them to the pan. Give them a nice sear on each side, a couple minute each.
Process the tomato cause and chipotles in adobo sauce in a food processor, then pour the mixture into the pan, covering the chicken.
Stir in the seasonings.
Bring to a quick boil, then reduce the heat and simmer for 30 minutes, or until the chicken is cooked through and easily pulls apart.
Remove the chicken and shred it with a couple of forks.
Return the chicken to the pan and simmer in the sauce another 5 minutes.
Preheat oven to 350 degrees.
Spoon some of the sauce from the chipotle chicken into a 10-inch baking dish or pan.
Lay half of the tortillas into to the dish, then spread half of the chipotle chicken over them.
Top with half of the shredded cheese.
Repeat with the remaining tortillas, chipotle chicken and cheese.
Bake for 20 minutes.
Remove, garnish and serve!