Arrange squid in a bowl. Add soy sauce, mirin, and lime. Marinate for 12 minutes.
Combine onion, tomato, ginger, salt, and ground black pepper in a bowl.
Stuff the marinated squid with scallions and onion mixture. Secure the head of the squid using a toothpick to prevent it from falling off.
Heat the grill and start to grill one side of the squid. Brush annatto oil on top of the squid. Continue to grill for 2 minutes.
Turn the squid over to grill the opposite side. Brush annatto oil on top. Continue to grill for another 2 minutes. Note: Flip the squid every 2 to 3 minutes until it gets fully cooked. Do not overcook squid as the texture will be tough and rubberlike.
Transfer to a serving plate. Serve with a dipping sauce composed of chopped onion, tomato, soy sauce, and vinegar.
Share and enjoy!