Stir in the onions and tomatoes, cooking until the onions become soft.
Add the squid to the pot and sauté for 2–3 minutes.
Transfer the squid to a separate bowl and set aside.
In the same pot, pour in the soy sauce and water. Bring to a boil.
Add the vinegar and allow the mixture to boil again. Stir, cover, and simmer for 3–5 minutes over medium heat.
Return the squid to the pot. Add sugar, salt, and black pepper. Stir well and cook for another 2 minutes, ensuring the squid remains tender (avoid overcooking).
Remove the squid using a slotted spoon and place it in a serving bowl.
Continue cooking the remaining sauce until it reduces by half.
Pour the thickened sauce over the squid and toss gently.