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- In The Doraemons Special, Nobita and Matadora uses the seven mysteries to scare off two robbers from the school at night with the help of their gadgets.
- In Urusei Yatsura, the teacher Onsen-Mark tries to do the traditional midsummer spook-the-youngsters-with-scary-stories routine and mentions the Seven Mysteries of Tomobiki High. Unfortunately, due to the weirdness magnets in the class (Moroboshi and Co.), most of these were already the subject of various previous chapters, and the class was bored.
- The girls in Strawberry Panic! do a similar investigation.
- Came up in Mahoromatic, with the added twist there actually was a ghost in a classroom.
- The Kindaichi Case Files story "Smoke and Mirrors" has "The Seven Mysteries of Fudo High." They all turn out to be rumors started to cover up dead bodies hidden in an old building that used to be a lab for a crooked pharmaceutics company. Not to mention there were originally six mysteries.
- Mai's arrival at Fuuka Gakuen in Mai Hi ME quickly becomes one of that school's seven mysteries.
- Appeared in the later seasons of Ranma ½, revolving around a "lost school store" and its aged keeper, "the Secret Don of Furinkan High" whose stories of the school's past tied into the Warring States era, WWII, the Mongol Empire, and the Napoleonic Wars (and were, of course, pure fabrication). A later episode introduced an actual ghost girl to haunt the place.
- In Mythical Detective Loki Ragnarok, the girl sidekick takes Loki to her school to show him their seven mysteries. As usual, only the last one lacks a mundane explation.
- In the Toei Animation version of Kanon, after discovering Mai fighting demons at the school, Yuuichi asks Kaori if she's heard of a girl that appears at night. Kaori thinks he's talking about the obligatory "cute girl ghost" of the seven mysteries. However, every single one is completely bogus, including the ghost; Mai's supernatural connections have a very different origin.
- One of The Seven Mysteries is the main cause of plot in Uta Kata. The rest don't show up.
- Dirty Pair Flash manages to set up a High School A.U. situation in its second season as an excuse for this plot. It turned out to be a "Shaggy Dog" Story and a "Scooby-Doo" Hoax as the school was part of a planetwide amusement park and the "ghosts" were All Part of the Show.
- The third episode of Fairy Musketeers revolves around the seven mysteries. They all turn out to be caused by the heroine, Akazukin.
- There are Seven Mysteries within Green Dolphin Prison in JoJo's Bizarre Adventure: Stone Ocean (which is actually set in Florida, not Japan) - one of them being the unusual and rare appearance of Louis Vuitton bags at the prison shop - however, they don't appear to have anything to do with the plot and are the least mysterious things about the dangerous prison.
- The school in Kekkaishi has 77 Mysteries. The increase is due to the school sitting on the manga's resident Applied Phlebotinum.
- One episode of Maria†Holic focuses on the seven mysteries of Ame no Kisaki Girls' School, a high percentage of them involving blood. To the surprise of no one, Kanako is directly responsible for all of them due to her fantasies. Kanako's homeroom teacher later tells her that the seven mysteries applying to the whole school change every year, but seven other mysteries about Kanako's dorm manager have never changed; they range from the genuinely mysterious ("what the hell is her real age?") to mundane Fridge Logic ("why are Virtual Boys not banned along with the other electronics?"). If anyone happens to learn all seven mysteries, the dorm manager will do...well, something, anyway.
- Ikki's school in Air Gear has seven mysteries, most of which are explained by the presence of a secret room Kogarasumaru eventually uses as their home base.
- Seitokai no Ichizon - Manga - The students confuse this with a scary story tournament, so the school ends up with dozens of mysteries, all horrifying. Minatsu undoes it all by adding the legend of the girl who goes around destroying all the ghosts. But Ken's story is the scariest:
Ken: Once upon a time there was a little maid called Kurimu who served her master with all her heart and all her body and all her soul. The end.
- Higanbana no Saku Yoru ni is all about a school's seven mysteries (and the creation of an eighth...), and, as such, has this entire subject as a Discussed Trope.
- A major plot point Dusk Maiden of Amnesia. The Paranormal Club believes that finding all seven mysteries will help them discover the secrets behind Yuuko's murder. Much of the plot involves distinguishing between rumors or ghost stories and true mysteries.
- One episode of the Sgt. Frog anime has Keroro setting up shop in an abandoned school, planning on staging a few ghost sightings and turning it into a tourist trap to help fund the invasion. He tests out his scheme on Fuyuki and Momoka, who happen to be in the same building on a ghost-hunting expedition, by throwing a set of seven (actually five) "school haunting" cliches at them.
- The first episode of Haunted Junction had the Power Trio searching not just for the Seven Spots, but for the seven ghosts associated to them. Hilarity Ensues.
- Nana Fushigi Gakuen actually used this as the title (literally, "Seven Mysteries High School") and featured a pair of ghostbusting schoolgirls. The staircase that has more steps going down than up was the Book Ends for the series.
- A series of omakes in the Bleach anime had Ichigo investigating seven unexplained phenomena in Karakura Town, which invariably turned out to be his friends dicking around.
- In My Monster Secret, the Seven Mysteries are specifically named, but the protagonists quickly realize that they're the Mysteries; the "Afterschool Vampire" is the series' female lead Youko Shiragami, the "Dwarf of the Hallway" is Class Representative Nagisa Aizawa (a doll-sized alien who pilots a Mobile-Suit Human), etc. However, eventually they realize that these legends have been around for years and thus must refer to the past generation — for example, the "Afterschool Vampire" isn't Youko but rather her father Genjirou.
- In Attack on Titan: Junior High, we have the "Seven Mysteries of Titan Junior High". Armin apparently is knowledgeable about them. As it turns out, they are a prank created by the Survey Club's members to make the test of courage more fun, but the seventh mystery appears to be true, since the ghost girl mentioned by Erwin is actually Frieda Reiss, implied to be a senior before she becomes a ghost.
- Shows up during an episode of The Devil Is a Part-Timer! as the characters are trying to find a way to get more magic. It turns out there's only six mysteries, since finding the seventh (allegedly) triggers a call on your cellphone which will cause you to disappear. Naturally, the heroes immediately ask:
- 1. How does anyone know what happens if you disappear as soon as you find out?
- 2. Why would a decades-old legend involve modern cell phones?
- Comes up between story arcs in Blue Exorcist. The mysteries range from strange noises coming from one specific toilet stall to a house that never seems to get closer as you walk toward it. In a subversion, all seven of them turn out to actually have supernatural origins, no matter how mundane they sound.
- The plot of the first Hatoful Boyfriend Drama CD is about Ryouta and Sakuya investigating the seven mysteries of St PigeoNation's.
- Kingdom Hearts:
- In Kingdom Hearts II, part of the extended prologue in Twilight Town features Roxas and his friends investigating "Seven Wonders" that appear to have mundane explanations, while the true explanations are quite extraordinary, the blanket explanation being that they're either glitches in the simulation or Nobodies screwing around with things on purpose... Well, except for the staircase one. Rai's an idiot.
- The Seven Wonders are also in the real Twilight Town in Kingdom Hearts: 358/2 Days, and inspecting Pence's notes reveals that they're all the same as the simulated Twilight Town's with similar mundane explanations, with the exception of an "Eighth Wonder," which turns out to be an invisible Heartless.
- In Paper Mario: The Thousand-Year Door, the Glitz Pit has its Seven Wonders that one of the NPCs tell you. It turns out that they are all true, and you must investigate them to advance the plot. Of course, in typical Mario fashion, these Seven Wonders have some humorous explanations and aren't all that mysterious given what Mario has seen in the past.
- A mission late in Crisis Core has Zack seeking out the seven wonders of Nibelheim, all of which have mundane explanations, and gets him a reward for figuring out.
- The third Mega Man Star Force game has "The Seven Wonders of Echo Ridge," despite there being only six, as mentioned by an NPC very late in the game, after no doubt having driven batty many players who thought to look for them all out of curiosity.
- Apparently, the Seven Mysteries of North High are the subject for Suzumiya Haruhi no Chokuretsu, a game released for the DS in Japan.
- In BlazBlue: Continuum Shift, Carl's Gag Reel has him recall the time he, Noel, Tsubaki and Makoto (who he was at the academy with) had him go through one of these because he was feeling homesick.
- In Yakuza 3, a series of subquests in Downtown Ryuugi centers around 'The Seven Mysteries of Ryuugi', as told by a group of gossiping schoolgirls. Inevitably, each of the mysteries turn out to either have a mundane explanation, or - more frequently - comes down to somebody running a scam. For the perfect punchline, the main character himself essentially turns into the Seventh Mystery - a 'ripped older guy' who shows up when people fall prey to loansharks or scammers to beat them up. Considering how invincibly badass Kazuma Kiryuu is, he's certainly closer to being supernatural than any of the other so-called mysteries...
- Tales of Rebirth features the "Seven Great Illusions", phenomena which the adventurer Franz is seeking. Three of them are sought during the main story, althoigh the "Garden of Illusion" is quite different from the one found during the story.
- There's an RPG Maker game called Seven Mysteries, though strangely it's only this trope for the first four chapters. The remaining three deal with the hero of chapter four trying to get to the bottom of everything. As it turns out, a psychotic student had killed seven classmates over a two-week period, framing his last victim, a shy transfer student, for his crimes. The girl's angry ghost was haunting the school, tormenting people who wandered in at night with horrific hallucinations. The headmaster knew about the haunting, but to avoid shutting the school down he conspired with the murderer to kill off the victims/witnesses and stockpile the bodies in a hidden room.
- Subverted in Fantasy Life: the seventh mystery of Castele is that Castele has only six mysteries.
- The Realm of Spirits in Blank Dream is themed around this. In order to reach your destination, you have to track down and experience six of the seven mysteries; the place where the mirror is locked away is considered to be the seventh.
- Thors, the military Academy of Adventure featured in The Legend of Heroes: Trails of Cold Steel, has a set of seven mysteries that your main character, Rean Schwarzer, can investigate in an optional quest. All of them turn out to be mundanities: a supposed graveyard that was really just a bad test paper a student buried "six feet under," a "haunted piano" that was really just being tuned, a supposed poltergeist that was just the result of frustrated cooks, etc. The twist is that there is apparently an entirely different second set of seven mysteries also taking place at the Academy that is only briefly alluded to. When Rean asks why she doesn't count the definitely mysterious Old Schoolhouse as one of the seven mysteries, Beryl, head of the Occult Research Society club, implies that of course it's included... in the real seven mysteries of Thors... In Cold Steel II, when the Reverie Corridor appears in the Old Schoolhouse, she tells Rean that he's fortunate to be one of the lucky few that gets to see the truth behind the 'eighth' of the academy's seven mysteries.