Prepare the Sauce: In a large bowl, whisk together the soy sauce, water, brown sugar, mirin, minced garlic, minced ginger, green onions, sesame oil, and crushed red pepper flakes (if using).

Marinate the Chicken: Place the chicken thighs in a large pot or Dutch oven. Pour the sauce over the chicken, ensuring that all pieces are submerged. Allow it to marinate for at least 15 minutes, or up to 1 hour in the refrigerator for extra flavor.

Cook the Chicken: Place the pot over medium heat and bring the sauce to a simmer. Cover and cook for 30-40 minutes, or until the chicken is tender and cooked through. Turn the chicken halfway through cooking to ensure even flavor absorption.

Reduce the Sauce: Once the chicken is cooked, remove it from the pot and set it aside on a serving plate. Increase the heat and let the sauce simmer uncovered for an additional 5-10 minutes, or until it has slightly thickened.

Serve: Serve the chicken over rice, spooning the reduced sauce over the top. Garnish with additional sliced green onions if desired.