To the bowl of a food processor add onion, habanero peppers, scallions, garlic, 2 tablespoons olive oil, soy sauce, lime juice, brown sugar, ginger, thyme, salt, cinnamon, allspice, nutmeg, and pepper. Process until smooth.
Place chicken into a large ziplock back and pour the sauce over the top. Seal the bag and move the chicken around to ensure that all sides are coated.
Transfer to the refrigerator for 3 hours, up to overnight.
When ready, preheat the oven to 375°F and line a large baking sheet with parchment paper.
Transfer the marinated chicken to the baking sheet.
Bake 40-50 minutes or until the internal temperature of the chicken is 165°F.
Set the oven to broil for the last 2-3 minutes if you prefer a good char.
Serve with rice. Garnish with limes and fresh parsley.