Marinate the Chicken:In a large bowl or resealable plastic bag, combine the soy sauce, water, brown sugar, garlic, ginger, onion, and red pepper flakes. Add the chicken thighs and turn to coat. Cover and marinate in the refrigerator overnight for best flavor (or at least 2 hours).
Prepare to Bake:Preheat the oven to 375°F (190°C). Transfer the marinated chicken to a baking dish and pour the leftover marinade over the top.
Bake Until Tender:Bake for 30 to 35 minutes, or until the internal temperature of the chicken reaches 165°F (74°C) and the sauce has thickened into a sticky glaze.
Garnish and Serve:Plate the chicken and spoon over the thickened glaze. Garnish with chopped green onions or sesame seeds, if desired. Serve hot with white rice, grilled pineapple, or a fresh green salad.