In a food processor, combine 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 in a large zip-top bag. Pour marinade over the chicken and seal. Move the chicken around to fully coat.
Refrigerate for at least 3 hours, up to overnight.
Preheat oven to 375°F. Line a large baking sheet with parchment paper.
Transfer chicken to the baking sheet, leaving space between pieces.
Bake for 40-50 minutes, or until the internal temperature reaches 165°F.
Broil for 2-3 minutes at the end for added color and char, if desired.
Garnish with parsley and serve warm.