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The Greatest Mystery Anime of the 1990s

When we think of anime, we often think of Sci-Fi, Romance, Mech, Horror, Action-Adventure, and Slice of Life stuff.  However, there are a lot of mystery-themed anime out there.

Most of these shows combine genres with the list above, so it would be normal to find a show that is Mystery and Romance (for example, 1996’s Fake).

In this article, we will touch upon 13 shows (in no particular order) that fit into the Mystery genre of 90s anime.

Side note: You can always spot a mystery show. How? It’s raining. (Thunderstorms are a bonus.)

Second side note: I am totally peppering this one with pop culture references. Get ready! Let’s have fun!

The Best Mystery Anime of the 90s

13. The Files of Young Kindaichi 

Kindaichi Shounen no Jikenbo – 1997

The Kindaichi Case Files is one of the ultimate whodunnit series! It began serialized in Weekly Shōnen Magazine and ran from 1992 to 2017. It is considered one of the earliest works in the mystery genre. Of course, it spawned an anime series and much more. A new series was released in 2018 and follows the characters after a time jump.

Renamed The Files of Young Kindaichi, the show ran on Nippon TV from 1997 to 2000 and it aired 148 episodes and one special edition. Two animated movies were also created and released by Toei.

The Files of Young Kindaichi followed the stories of Hajime Kindaichi a lazy high school student with a high IQ and adeptness in solving mysteries and gruesome murders.

Sadly, most people judge him poorly for being an unmotivated slacker. Miyuki Nanse is his neighbor and a perfect student. She sees him for who he truly is.

After watching a couple of episodes recently, I made note of an important detail…it was raining. 😊 Also, the murderers are often real people with real issues and not psychopaths. This makes for much more interesting stories.

12. The Big O

The Big O – 1999

Often labeled as Mech-Noir or Tech-Noir (I love that term), The Big O is a combination of genres. You could call it action-adventure, sci-fi, mech.. etc. That being said, the entire plot is based on a mystery.

Forty years prior to the story, there was an “event” that destroyed much of the world and left the survivors with amnesia.

Cool premise, right?

The story’s main character is Roger Smith. He is a negotiator for the city of Paradigm and he works with a female android who he is also the caretaker for.

Roger is a slick Bruce Wayne-looking guy which fits because the anime has a Batman the Animated Series style to it.  Even Paradigm city has a polished Gotham feel to it.

Roger also has a cool Batmobile… I mean, it’s a special car, more like something James Bond would drive.

One thing Roger Smith has that Bruce Wayne doesn’t is a giant robot Megadeus called Big O, which is helpful when other giant robots or kaiju-looking things attack.

All he needs to do is speak into his watch and say, “Showtime!” Which is kinda like when Michael Knight called to K.I.T.T. (I feel comfortable with this reference because Knight Rider ended not long before the 90s began.)

In this story, the characters seek to remember and decipher their mysterious pasts. Since it is only 26 episodes, it can be a quick and easy show to binge-watch.

11. Black Jack

Black Jack OVA – 1993

I was not expecting to like Black Jack. I judged the old book by its cover, or anime show by its main character’s dumb hairstyle and Frankenstein’s monsters scars and Dracula cape…

But wow, I kinda loved this one after watching it. I must admit, I just watched it for the first-time weeks ago and then binged much of it afterward.

Black Jack is a Medical Mystery Seinen anime, or would it be Seinen Medical Mystery anime?  Your choice, I guess. 😊

Regardless, Black Jack comes with a nudity warning. Nothing too graphic, just a flash of boobs each episode. Sometimes, it felt unnecessary, other times, it fit into the story, like when the freedom fighter woman showed the doctor her scars, so he could understand the sacrifices she had given to her home.

But who is Black Jack? Well, he’s what you would consider a mercenary. He’s a highly skilled doctor for hire, and is often sought after for rare ailments or jobs steeped in danger. He’s intelligent with nerves of steel and the ability to defend himself if needed.

It is also important to note that he is loved by the ladies. It seemed like they were always throwing themselves at him for one reason or another. But Black Jack is anti-social and seems to only care about his loyal assistant Pinoka, who is also his adopted daughter and the result of a parasitic twin case.

Um, yeah, she’s a Teratogenous Cystoma (a growth the TV’s Pimple Popper might commonly call a teratoma). It’s a long story, but one worth watching to understand further.

The thing that stands out the most in these exciting episodes is the sheer volume of medical terms. Black Jack often explains the medical mystery as he solves it or operates, and the terms he uses are right out of Grey’s Anatomy, and wow, it just legitimizes the show.

10. Case Closed

Detective Conan – 1996

Case Closed (also known as Detective Conan) is a massively popular manga and anime. The manga has run from 1994 to the present with over 102 volumes.

The anime premiered on January 8, 1996, on Nippon Television Network System in Japan and has been airing from 1996 to now with over 1,065 episodes. Impressive, right?

This is a multi-media giant with films, OAVS, audio CDs, video games, and TV specials.

Case Closed is the story of a high school detective, Jimmy Kudo, who was de-aged by a drug. Now he’s in grade school.

He acts like a combination of Sherlock Holmes and Jessica Fletcher, gathering people in one room to explain how he solved the mystery.

OK, I am slightly ashamed of that reference, but if you know where Jessica Fletcher comes from, then maybe you see my point, and it’s nothing for me to be embarrassed by at all.

I will admit that I did not watch many episodes of this one, so I’m no expert on how the story progresses through the 1000-plus episodes. But if this style of mystery anime is your thing, then you have a great wealth of media to enjoy.

9. City Hunter ‘91

City Hunter ’91 – 1991

City Hunter is another huge franchise that has awarded us with all sorts of media tie-ins and adaptations. City Hunter ’91 was released in 1991 and only has 13 episodes, but if you like it, it is only a small part of a larger world.

City Hunter’s intro feels like a James Bond opening but with a Vegas flavor to it. I gotta say, I like it! The show itself feels like something that would have been a fun 80s or 90s TV show like Miami Vice and star an icon like Bruce Willis or Jean Claude Van Damme.

Dare to dream…

Anyway, the show features Ryo, a skilled marksman with as many weapons as you can list, although he prefers his .357 Magnum. He’s a private investigator as well as what we in the fiction writing business call, thanks to the Great Bard, a lothario (manwhore in current urban dictionary terms). 😊

Kaori is Ryo’s steadfast partner and is often annoyed by his flirtatious ways. She helps the P.I. business by arranging clients and keeping the books. She’s a valuable part of the team, and together they are well-balanced.

City Hunter ’91 has a feel-good 80’s anime style and is hard not to like.

8. Clamp School Detectives

Clamp Gakuen Tanteidan – 1997

Clamp School Detectives features the all-girl manga art team called CLAMP. It had three volumes published via manga in the early 90s, before releasing in anime format in 1997 for one season (27 eps.) produced by Bandai Visual and Studio Pierrot.

This lighthearted comedy show is about a group of little boy detectives that are girl crazy. It has a JPRG animation feel to it.

I could not help but see one character as the Bard/Scholar, another as the Fighter, and the last one clearly as the Thief.

Combined with those tones, there was a slight Hardy Boys feel. (OK, you might have to look that one up.)

Each episode of Clamp School Detectives had a standalone mystery to be solved, and guess what, if there were maidens in distress, these boys were there to help and save the day!

What more can I say about this entry on our mystery list? Well, if you are into shows with cutesy kid detectives, this is the one for you! Many people refer to it as a fun old series in their reviews. Give it a try, you might like it.

7. Fake

Fake – 1998

Fake starts off raining with a thunderstorm brewing. Clearly, we are being welcomed to a thrilling new mystery.

We watch as a person flees from someone with a knife. But they can’t escape and get stabbed to death. Brutal. This is not a case for the Clamp School Detectives, no sir! This feels like some harsh real-world shit. Or at least maybe a real KOEI world, cause the animation looks a little like Fatal Fury 2, which I can respect.

Fake is a one-hour OAV based on a two-volume manga series by the same name.

We are quickly introduced to the two main protagonists, Randy (Ryo) McClane and Dee Laytner. They are New York City cops on vacation in England.

It does not take long to realize this trip is more than just a vacation, it’s a way for Dee to further express his feelings for Ryo in hopes of deepening their relationship. 

This is a true multi-genre mystery series. It has elements of Romance, Supernatural, Yaoi, and touches of comedy. 

Released in 1996 by Media Blasters, Fake is heavy on dialogue and drama, both of which push the story forward for the full hour. It’s worth your time just to experience well-developed characters with amazing chemistry.

Hey! I wonder if Randy is related to another famous McClane cop from New York? Hmm…

6. Master Keaton

Master Keaton – 1998

Guess what? Master Keaton starts off with rain. 😊

Then it appears someone has fallen off a cliff. That’s a terrible accident, or maybe it was a murder. You know what we need? An investigator…an insurance investigator!

Our enigmatic insurance investigator goes by the name Taichi Keaton, and he has a real James Bond look and style about him. He is also an archaeology teacher and likes to use some MacGyver-like skills in a refreshing real-world setting.

He even works for Llyod’s of London, which is a real company that was founded over 300 years ago. Like for real-real. Like really-really world real. Cool, huh?

There’s much to like about Master Keaton. It has a long history; 18 volumes of manga running from 1988 to 1994, which makes it one of the best-selling series.

Madhouse brought the anime to life. It ran for two seasons with 39 episodes and, for many, felt like a walking-talking manga.

If you are looking for a dialogue-driven mystery-adventure-thriller that is aimed at children of the 80s (because of our age, not our pop culture preferences), this is one for you.

5.  Mobile Police Patlabor 2: The Movie

Kidou Keisatsu Patlabor 2 the Movie – 1993

Mobile Police Patlabor 2: The Movie (more commonly known as Patlabor 2) was directed by Mamoru Oshii, who also directed the original Patlabor: The Movie and the landmark film Ghost in the Shell.

Released in 1993, the movie won the best-animated film award at the Mainichi Film Concours Awards. In fact, Patlabor 2 is considered one of the best-received anime movies of all time due largely to its excellent artistic qualities, largely the outstanding layout and framing work.

However, do not expect tons of action and adventure in this one, it’s more of a Tom Clancy-style thriller.

How does it fit into the mystery genre? With its fullness of political intrigue and suspicious military actions.

For those unfamiliar with the series, let me summarize it here. It is set in an alternate post-WWII timeline where the US and Allies occupied Japan. The country is rebuilding and repairing itself after the long occupation.

In order to keep the peace, the Metropolitan Police force has cutting-edge mechs called “Patlabors.” But there are still issues out there to overcome due to growing political concerns and burgeoning terrorism.

I don’t want to say too much so as not to spoil this intellectually stimulating gem. But I can say it is worth a watch or two.

4. Nightwalker: The Midnight Detective

Night Walker: Mayonaka no Tantei – 1998

Now back to our junk food anime diet with a dark and gritty sugary treat!

Nightwalker: The Midnight Detective is a 1998 horror – mystery – adventure about a vampire private investigator who protects humanity from other demons called Nightbreeds.

Fans of Joss Whedon’s Buffy and Angel shows should enjoy it, as Angel was a private investigator helping the helpless from demons and other baddies in his 1999 show.

Nightwalker’s lead character is Shido, an old vampire with a complex and mysterious past filled with atrocities he would like to forget. But Shido has decided to fight the good fight and protect people now as a private investigator and demon hunter. 

Riho works with Shido as his receptionist and secretary. She has a dark past too, which is very interesting and important to anime as a whole. See, Nightwalker delivers us with some very contrasting female characters, starting with her.

As the story progresses, we see how toxic relationships, doubts, and hard-made decisions are the prevailing themes.

Shido is full of regret and has had a very toxic relationship with a former male coworker. Riho is troubled by her past and, for much of the series, is unaware of how her sad history is directly linked to Shido’s actions.

Regardless of not making huge waves in anime fandom, there is a cult following and a lot of videos on YouTube where people mix popular songs with clips from the show.

3. Puppetmaster Sakon

Karakuri Zoushi Ayatsuri Sakon – 1999

Karakurizōshi Ayatsuri Sakon started off as a manga title like most anime. It ran for four volumes before Tokyo Movie Shinsha produced the show as Puppetmaster Sakon, which ran for 26 episodes from 1999 to 2000.

The main character is Sakon Tachibana, a master ventriloquist and puppeteer. He likes to travel the world and solve mysteries with his puppet and best bud, Ukon.

Ukon is a 100-year-old doll that looks like a child. When Sakon operates him, the puppet appears to come to life. Ukon has another ability or special power, the souls of recently dead can possess him and give messages to Sakon.

Are you still with me?

It’s a strange and unique show. Sadly, it is filled with boring and cliché storylines and so many ham-fisted hints that it’s hard not to solve the mystery before Sakon does.

To be honest, this is a weird one for me. I was confused by the characters at first. I thought it was a woman and a younger girl, maybes sisters by the close proximity that they stood to each other. Then, as I paid closer attention, I realized…whoa, that’s a freaky puppet!

If a magical puppet supernatural mystery is what you are looking for, then you will find it here.

BTW, check out the B-movie Puppet Master from 1989 as another option…or maybe not. That one is all sorts of terrible. 😊

2. Steam Detectives

Kaiketsu Jouki Tanteidan – 1998

Steam Detectives ran on Japanese television from 1998 to 1999 with 26 episodes and was later licensed by ADV Films for North America.

This story follows a gun-toting boy genius named Narutaki, and his robot in a world that’s only fuel source is coal, and only power comes from steam engines.

One thing is clear in this interesting era of steam–crime is rampant, so get ready for lots of action in this mystery-thriller.

Steam Detectives’ art is similar in style to Japanese Role-Playing Games like the highly popular Persona series.

If you like stories featuring mech, you are in for a treat: steam-powered mech are kinda the coolest. 

Narutaki investigates in a style like Sherlock Holmes, has Inspector Gadget-like gear, and a past similar to Batman.

But his best resource is Ling Ling, a nurse who looks after his health and owns the robot that aids him. Also at his side is Kawakubo, his loyal butler and mechanic for all those times his giant robot needs repairs.

Steam Detectives has a very flashy collection of characters and villains, often looking like something out of a superhero show aimed at younger kids. 

1. Tokyo Babylon

Tokyo Babylon – 1992

Tokyo Babylon originated as a manga series, which quickly became an anime show and later graduated to a live-action movie. Also, by the CLAMP all-girl team, Tokyo Babylon is dark and gritty with animation that has an Akira or Bubblegum Crisis feel to it at first glance.

Two OAVs were released; one in 1992 and another 1994, animated by Madhouse. Later, US Manga Corps released the videos in the USA in 1995.

Tokyo Babylon follows Subaru Sumeragi, a powerful sixteen-year-old magician.

He is also the 13th head of a prominent family that faithfully served the emperor for centuries.  This is why he is often called to solve occult mysteries and fight evil spirits with the aid of his twin sister and best friend/romantic interest.

While the basic plot of Tokyo Babylon is simple, and a lack of character development is often faulted, the subplots and themes, along with the interesting costumes, are what most people find interesting.

I did not find this one very engaging, but I soldiered on. The two OAVs aren’t very long, and let’s admit it, I have spent my time watching worse. (Like Luther the Geek or Beloved.)

Fair warning: ready your remote when you reach the middle of the OAV. A song will start to play. You might want to mute it. Save yourself, like the kids say. However, if you can endure the song, more power to you!

Mystery Anime Conclusion

There are many options out there for 90s anime thriller-seekers. Some are short, easy-to-watch, and binge-worthy. Others will require some investment of time.

Our best advice is to start off with a mystery that is combined with another one of your favorite genres.  We bet you’ve already watched a few and not even realized it.

Also, wear a weather-resistant jacket because it’s most likely going to be raining out there. lol

Kevin Breaux

Kevin James Breaux is an award-winning author who has written nine books and devoted over fifteen years of his life to crafting short stories and novels. See his work at:

This Post Has 2 Comments

  1. Billy Dale Green

    As an old school fan of old school anime, I truly enjoy Mr Breaux’s articles. His on-color descriptions of shows and characters confirms that he’s a true fan, as well. Best part, he talks to the older original audience; not the tweens trying to sound cool on tic-toc.

  2. Billy Green

    You can always spot Kevin Breaux articles. How? There interesting before you even start reading. I love the way this guy writes; it’s like he’s having a conversation with you about your shared favorite memories.

    1. Billy green

      And yes, I read the article twice!! What can I say; I’m a fan.

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