Pat dry the chicken thighs and season both sides with salt and pepper.
In a large skillet over medium heat, heat olive oil. Sauté onion for 5 minutes until softened; add garlic and sauté for another minute.
Stir in tomatoes (with juice), cocoa powder, minced chipotle peppers, and chicken broth. Simmer for 10 minutes.
Nestle the seasoned chicken thighs into the sauce. Cover and reduce heat to low; simmer for 25 minutes until cooked through.
Remove the chicken, shred it with two forks, and return to the sauce to soak up flavors.
Serve over rice or warm tortillas drizzled with extra sauce.