The Secret Box is an item that is not seen during the main game, and is only seen after finishing the game and revisiting chapters. Whenever Obtaining a Secret Box, Neku will state "Oh, Snap!". Each Box has an item to give, and if you have already collected the item, Neku will get a Yen Pin.

Neku Box

Spoiler warning: Plot and/or ending details follow.

Ken Doi Edit

Ken Doi, the owner of Ramen Don, will on Week 3, Day 7 give you a Samurai Helm, and if you trigger the Secret Report Event again, he will give Neku a box, where Neku ponders about whether or not Ken Doi is the man responsible behind the Secret Boxes.

Spoiler warning: Spoilers end here.