"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!

By the Clock Keepers’ decree, the past has been rewritten, creating a new future…and suddenly, Nene finds herself in a world very different from the one she knew. The relationships between her friends are all mixed-up, her love life is in shambles, and Hanako-kun is nowhere to be found! Meanwhile, a strange rumor spreads through Kamome Academy about a ritual to summon a wish-granting supernatural. But is this little boy just lonely and looking for a playmate, or is there something more sin...

EXPOSÉ! FIND OUT WHAT THE SCHOOL MYSTERIES DO AFTER SCHOOL! The ghostly Hanako-kun and his mortal assistant, Nene Yashiro, usually have their hands full resolving various supernatural incidents in Kamome Academy, but how do they spend their time when they get a break from all that? Come and watch the characters of Toilet-bound Hanako-kun play games, get sick, change genders, and discover world-shaking secrets during their laid-back after-school hours!

Nene steps into the spotlight! The mermaid kingdom hasn't forgotten her, and they're back to claim what's theirs! Can Hanako protect her from becoming permanently fishy? Meanwhile, Kou makes friends with an odd ghost haunting the entrance to the middle school division. Kou has no idea who this guy was when he was alive, but that doesn't mean he can't help him solve his unfinished business! Will the junior exorcist be able to help this friendly ghost pass on...?

The big clock that governs Kamome Academy’s time is destroyed— a sin the Clock Keepers won’t easily forgive. When Akane is called upon to fulfill his duty, he sheds his identity as student council vice president and steps into the role of the lowliest Clock Keeper—the guardian of the present. With all three judges in attendance, a trial is to be held in the Clock Keepers’ boundary. Who is guilty? How shall they be punished? And…what must the guardians of time do to set things right?

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!?

At long last, Hanako-kun reveals his plan to save Nene from her inevitable, swiftly approaching death. But even knowing his intentions, Nene is determined to return to reality-and to do that, she’ll need the help of School Mystery No. 4, Mei Shijima. Can Nene help this spirit overcome her regret and self-loathing and find her way home?!

Nene Yashiro has made a pact with “Hanako-san of the Toilet,” aka Hanako-kun, to hold off the curse that has been placed on her. In exchange, she has to help him resolve the problems caused by the school’s supernaturals—starting with rescuing her friend Aoi from the clutches of the Misaki Stairs, one of the infamous Seven Mysteries. Can they reach the innermost depths of the Stairs before time runs out? And if they do, what dangers and secrets await them there...?

It's autumn at Kamome Academy, and the annual school festival is underway. While Nene and her friends are busy with preparations, a select few begin carrying out their plot in the shadows—they have their eyes set on the yorishiro of No. 1 of the seven School Mysteries, the Clock Keeper. When supernaturals burst onto the scene, what was supposed to be a fun school festival turns into an unexpected crisis...!

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!

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!?

That day, Nene went to school as usual, but found Hanako-kun acting like one of her normal classmates...!? She seems to be the only one who notices anything amiss, seeing as Hanako-kun was supposed to be a ghost...! Hunting for the truth, she heads to a mysterious tower. Fact and fiction clash in this Seven School Mysteries ghost story!