In a food processor, blend onion, garlic, chipotle pepper and adobo sauce, oil, lime juice, oregano, and cumin until smooth. Season with salt and pepper.
Add marinade and chicken to a large resealable plastic bag and rub all over to coat chicken. Let marinate in the fridge at least 2 hours.
Bring chicken to room temperature and preheat grill to high. Remove chicken from marinade and discard marinade. Grill chicken until cooked through and internal temperature reads 165°, about 8 minutes per side.
Serve chicken over rice with desired toppings.
