Through the workings of the School Mystery Clock Keepers, Kamome Academy's entire student body is covered in wrinkles!? To restore peace to the school, Hanako-kun teams up with a certain someone. Just when they thought the case was headed to its conclusion, the secret of Hanako-kun's assistant Nene is brought to light! What could it possibly be!?

After going to rescue Aoi, Hanako-kun and Nene are thrown from No. 6’s boundary and suddenly find themselves in a strange village, where they meet a girl named Sumire who seems to have a history with No. 6. Witnessing Sumire’s “wedding day” up close might just give Nene a hint on how to resolve the school’s impending crisis and save Aoi—but she’ll have to survive it first! Meanwhile, on the very banks of the Far Shore, Aoi and Akane finally put into words exactly what they mean to each other...

If Nene and Kou want to return to their own world, they have to kill "Amane Yugi" and "Sousuke Mitsuba"-or rather, the versions of them living within the canvas of Number Four's boundary. Faced with that cruel choice, Nene instead proposes a way to escape from this fake world to the boy she can't help but call "Hanako-kun." At the same time, Kou tries to win over Mitsuba as well-but just who exactly is this "Mitsuba"?!

"Hanako-san, Hanako-san...are you there?" At Kamome Academy, rumors abound about the school's Seven Mysteries, one of which is Hanako-san. Said to occupy the third stall of the third floor girls' bathroom in the old school building, Hanako-san grants any wish when summoned. Nene Yashiro, an occult-loving high school girl who dreams of romance, ventures into this haunted bathroom...but the Hanako-san she meets there is nothing like she imagined! Kamome Academy's Hanako-san...is a boy!

Nene Yashiro serves as the assistant to the School Mystery Hanako-kun. When she is invited by enigmatic playboy Natsuhiko to a mysterious tea party, she meets Hanako-kun's "girlfriend" and his "little brother"...!? On top of that, she learns that one of the Seven Mysteries is mixed in with her classmates...

It's been three days since they returned from the School Mystery Three, the Hell of Mirrors. To cheer up the depressed Kou, Nene heads to the Boundaries' Tanabata festival. She was supposed to be enjoying the festival with Hanako-kun and Kou, but suddenly she finds herself in the world 50 years in the past. And who should she meet there but Hanako-kun when he was alive!?

Nene and Kou want to learn more about their mysterious friend, Hanako-kun--and what better way to do that than school mystery number five, The 4pm Bookstacks! The rumors say that a secret door in the library leads the way to a supernaturally special collection. The Bookstacks know everything about everyone who's ever attended Kamome Academy--past, present, AND future! But whatever you do, don't read the red books...or your future will be drenched in blood!