Rated List of Mystery/Crime/Detective J-Dramas: My pick
Biases:
1) I don't like Detective Conan style stories (that mix of Agatha Christie and Conan Doyle where the focus is on the elaborate but unlikely puzzle while characters motivations are cursory).
2) This is a list of modern dramas.
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1. MIU 404
Japanese Drama - 2020, 11 episodes
This is the best mainstream J-drama of 2020. It's from the crew behind Unnatural and it was made after the writer Nogi-san watched Dele (and felt jealousy). It's hard to pick the best out of MIU, Unnatural, and Dele, but for the time being I can't put MIU anywhere else but on the top.
Fresh, genre-bending, suspenseful, fast-paced, heart-warming/heart-wrenching, fun, insanely well-made, elegant in its seeming simplicity, multi-layered, realistic - I can talk about MIU forever so don't hesitate to message me to fangirl)
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2. Unnatural
Japanese Drama - 2018, 10 episodes
This is the kind of mystery drama that could only be done in Japan. South Korea has Signal, Great Britain has Sherlock, and Japan has Unnatural.
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3. dele
Japanese Drama - 2018, 8 episodes
Yamada Takayuki and Suda Masaki aka the best of the best star in a short drama with superb script, directing, set design... Well, everything here is top-notch.
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4. Keiji Yugami
Japanese Drama - 2017, 10 episodes
This is the charming low stakes buddy cop drama with charismatic leads (Asano Tadanobu and Kamiki Ryonosuke) that features more female characters than other dramas on this list combined.
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5. MOZU Season 1 - Mozu no Sakebu Yoru
Japanese Drama - 2014, 10 episodes
Watch it for the outstanding cast, the plot turns, the suspense. But mostly, watch it for the style. Don't take it too seriously though and beware of the problematic stuff typical of the time period.
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6. HERO
Japanese Drama - 2001, 11 episodes
This is not a typical detective drama but it is a classic mystery show. It has charismatic leads, top-notch comedy, and touching stories. It could very well be in the first place.
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7. Odoru Daisousasen
Japanese Drama - 1997, 11 episodes
This drama is a gold standard of police procedural comedy. It established classic tropes that procedural J-dramas still rely on to this day but it arguably remains superior to most of its successors. Watch it for the great main conflict and the chemistry between the charismatic characters that embody different sides of this conflict.
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8. BORDER
Japanese Drama - 2014, 9 episodes
This one is for true detective lovers. Dark atmosphere and the fatalism of the hero remind one of the film noir. Beware of the slow pace, though.
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9. Kinkyu Torishirabeshitsu
Japanese Drama - 2014, 9 episodes
Glorious Amami Yuki stars in the brilliantly written mystery drama that also boasts the great pacing and the veteran actors cast.
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10. Joker Yurusarezaru Sousakan
Japanese Drama - 2010, 10 episodes
This is the best procedural-on-the-budget that I've seen. The suspense of the central arc, in particular, is amazing.
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11. Ryusei no Kizuna
Japanese Drama - 2008, 10 episodes
It's Kudo Kankuro's take on the mystery genre (with little comedy, though). It is a high-quality mystery that would be more appealing to those who appreciate well-developed relationships more than the fun of puzzle solving. Not that puzzle-solvers would guess the murderer...
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12. Bloody Monday
Japanese Drama - 2008, 11 episodes
Neck-breaking pace, cute leads, charismatic antagonists - this drama is high on the entertainment if you can forgive it the way it uses a flying bird as a metaphor for hacking.
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13. BOSS
Japanese Drama - 2009, 11 episodes
This is a complete fluff. It's funny and entertaining. Beware of problematic jokes.
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14. MR. BRAIN
Japanese Drama - 2009, 8 episodes
You either can take this seriously or you can't. In the latter case you could still enjoy it. The characters are charismatic and the pace is fast.
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15. Aibou: Season 11
Japanese Drama - 2012, 19 episodes
Aibou is the staple of low stakes watch-it-everyday-while-you-eat-dinner detective shows. The mysteries are well thought out if old-fashioned and the murderer is very hard to guess. Eleventh season features devastatingly handsome Narimiya Hiroki who is conspicuously put into unnecessary tight clothes every episode.
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16. ST Aka to Shiro no Sousa File
Japanese Drama - 2014, 10 episodes
This show is a hot mess. Watch it for the classic buddy cop shenanigans, the great cast, and the main character arc that is very funny from the genre perspective (see the movie for the finale).
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17. Rinsho Hanzai Gakusha Himura Hideo no Suiri
Japanese Drama - 2016, 10 episodes
This is a very low quality drama. Watch it for the buddy cop shenanigans but approach with caution.