Season the chicken on both sides with salt and pepper.
Heat a tablespoon of the oil in a large skillet over medium high heat. Once hot, add the chicken and cook, turning once, until browned, about 8 minutes. Transfer the chicken to a plate and set aside.
Add the remaining tablespoon of cooking oil to the skillet. Add the onion. Cook over medium heat, stirring occasionally, until the onion is softened, 5 minutes. Add the garlic and cook until fragrant, about 1 minute.
Add the tomatoes, chipotle, and chicken broth. Add the chicken back to the pan. Bring to a boil then simmer, stirring occasionally, until thickened and slightly reduced, about 15 minutes.
Then take it off the heat, remove the chicken, and let the sauce cool for a few minutes. Pour the sauce into a blender and puree until smooth (be sure to keep the lid open slightly to let out steam while you blend). Taste and adjust seasoning.
Shred the chicken, then return it to the skillet with the sauce and cook at a simmer until the meat is tender and the sauce is thick and darkened, about 20 more minutes.
Heat the tortillas in a skillet on the stove or in the microwave.
Spoon some of the chicken onto each tortilla and sprinkle with the crumbled Cotija. Garnish with green onions and chopped cilantro.