Arrange chicken in a large oven-safe skillet without overlapping pieces, skin side down.
Combine Japanese sake, soy sauce, sesame oil, and sugar in a bowl. Mix well until sugar is fully dissolved. Pour into the skillet with the chicken. Add ginger, garlic, shallot, and chili pepper.
Bake at 300 F (150 C) for 40 minutes.
Transfer the skillet to the kitchen counter. Flip the thighs so that skin side faces up.
Continue baking at 300 F (150 C) for another 20 to 30 minutes, until the thickest part of the biggest thigh registers 165 degrees F (74 C). Transfer the skillet to the kitchen counter.
Turn on broiler or turn oven to its highest temperature.
Use a ladle to skim oil from the surface of the sauce (*see footnote 1). Add basil leaves and serrano peppers.
Return the skillet to the oven and bake until the skin is crisped and charred, 2 to 4 minutes. Leave the oven light on and watch closely during the process. I found that baking time can vary a lot depending on the oven model.
Transfer the skillet to the kitchen counter and let rest for 5 minutes.
Serve over steamed rice or other preferred side with sauce while warm.
Alternatively, you can transfer the chicken to a plate, skim the oil with an oil separator, and place the chicken back in the skillet. The oil will be removed more thoroughly this way.