Mix chopped onion, soy sauce, brown sugar, garlic, sesame oil, and black pepper in a large bowl to make marinade. Add chicken thighs; soak for at least 20 minutes.
Spread onion rings on the bottom of a large pot. Place chicken thighs, with some of the marinade, on top. Pour in water to fill the pot halfway. Bring to a boil; reduce heat to medium-low and cook until chicken thighs are tender, about 1 hour 30 minutes. Add carrots and jalapeno peppers. Cook until carrots are soft, about 30 minutes more.