School Mystery No. 1’s Clock Keeper of the future has gone out of control, turning Kamome Academy’s entire student body into wrinkly old people! Hanako-kun, Nene, Kou, and Akane will have to work together to catch this agile trickster and keep the school from becoming a retirement home. But just when they seem to have Mirai cornered, one final prank goes horribly wrong, bringing Nene’s secret out into the open...

Kou has seemed depressed ever since he, Nene, and Hanako-kun returned from the Hell of Mirrors three days prior. To cheer him up, the three friends decide to go to a Tanabata festival held within one of the school’s Boundaries. But instead of getting to enjoy the festival with Kou and Hanako-kun, Nene is suddenly whisked off to fifty years in the past-where she finds herself face-to-face with a living Hanako-kun?!

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...

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?!

On a day like any other, Nene goes to school only to find Hanako-kun acting like one of her normal classmates...?! Weirder still, even though he’s supposed to be a ghost, nobody seems to find the presence of this so-called Amane-kun strange at all. Nene is determined to get to the bottom of this, and her search leads her to a mysterious tower...

"Thanks to the manipulations of those in the broadcast room, Nene and Sumire find themselves trapped once more in No. 6's boundary. While Hanako-kun isn't there to help them escape this time, they aren't alone-No. 6 himself is there as well! Sumire is thrilled to be reunited with her beloved after so many years, and with No. 6 having come to terms with his feelings at long last, perhaps they have a chance to change how they left things..."--

"After being ripped apart by the severance between this world and the next, Nene and Hanako-kun are finally reunited. That being said, it's not exactly a happy reunion. With their emotions running high over the seemingly intractable problem of her nearly depleted lifespan, they're all too quick to give in to anger. Meanwhile, as the Minamoto brothers have a spat of their own, No. 6 shows up out of nowhere--and he's out for blood..."--

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 No. 4’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...but just who exactly is this “Mitsuba”?!

"In exchange for a life, the link between this world and the next has been severed. Even so, Nene and Kou continue looking for a way to reach the boundaries, a search that leads them to the cursed "Red House." Inside, they find a boy who looks just like Hanako-kun and may have the answers they've been looking for-but they soon find the Red House is much easier to enter than to leave...!"--