Bring a pot of water to boil in a medium saucepan, then add the Baking Soda (1 tablespoon).
Slowly add the Egg (6) into the boiling water using a large spoon or soup skimmer. Allow to cook for 7 minutes.
Transfer the eggs into an ice bath and allow them to chill for 3 minutes.
Combine the Water (2 cup), Teriyaki Sauce (1 cup), and Mirin (1/4 cup) in a bowl or container with a tight-fitting cover.
Place the eggs in the teriyaki sauce mix. Cover the top of the eggs with a paper towel to help the liquid reach the eggs evenly all around.
Sprinkle the Bonito Flakes (1 handful) on top of the paper towel (if using).
Cover and refrigerate overnight. Remove the eggs from the seasoning liquid after 24 hours, or they will become too salty. Store in the refrigerator for up to a few days.