Best Nintendo 3DS Mystery Games of 2025

James Ryan Avatar
James Ryan
Last Updated: Jan 8, 2025

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Nintendo 3DS Mystery Games are a collection of captivating games that will keep players on the edge of their seats. With titles like "Detective Pikachu" and "Professor Layton and the Azran Legacy," these games offer intriguing storylines and challenging puzzles. "Phoenix Wright: Ace Attorney Trilogy" allows players to step into the shoes of a defense attorney and solve crimes in court. "Corpse Party" is a horror game that takes place in a haunted school, while "Zero Escape: Virtue's Last Reward" is a thrilling visual novel that presents players with tough decisions to make. These mystery games are perfect for those who enjoy solving puzzles and unraveling complex stories.

At a Glance: Our Top Picks

Pokemon Super Mystery Dungeon - Nintendo 3DS Cover #TOP 1
Pokemon Super Mystery Dungeon - Nintendo 3DS
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Pokémon Mystery Dungeon: Gates to Infinity - 3DS Cover #TOP 2
Pokémon Mystery Dungeon: Gates to Infinity - 3DS
ftb score rating icon 9.8
Nintendo 3DS Pokemon Super Mystery Dungeon Cover #TOP 3
Nintendo 3DS Pokemon Super Mystery Dungeon
ftb score rating icon 9.6

Top 10 Nintendo 3DS Mystery Games

Pokemon Super Mystery Dungeon - Nintendo 3DS

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Pokemon Super Mystery Dungeon - Nintendo 3DS Cover
Pokemon Super Mystery Dungeon - Nintendo 3DS Standard Edition

Befriend and explore ever-changing mystery dungeons with a group of 20 Pokémon, including starters and Pikachu, as players are transformed into a Pokémon and sent out to a world inhabited by only Pokémon. Interact with all 720 known Pokémon while attempting to save the world.

What We Like
Opportunity to choose your Pokémon and partner Pokémon from a group of 20, including starters and Pikachu
Interact with all 720 known Pokémon
Explore ever-changing mystery dungeons with your Pokémon friends

Pokémon Mystery Dungeon: Gates to Infinity - 3DS

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Pokémon Mystery Dungeon: Gates to Infinity - 3DS Cover
Pokémon Mystery Dungeon: Gates to Infinity

Experience the vibrant 3D graphics and detailed environments of Mystery Dungeons as a Pokémon in Pokémon Mystery Dungeon: Gates to Infinity. Build your own Pokémon Paradise and befriend other Pokémon as you battle, collect treasure, and explore the ever-changing dungeons. Discover new Mystery Dungeons in the real world using the Nintendo 3DS Camera and explore them with up to three other players.

What We Like
Vibrant 3D graphics and detailed environments.
Build your own Pokémon Paradise and befriend other Pokémon.
Ever-changing Mystery Dungeons with new adventures around every corner.
Discover new Mystery Dungeons in the real world using the Nintendo 3DS Camera.
Explore Mystery Dungeons with up to three other players.
#TOP 3

Nintendo 3DS Pokemon Super Mystery Dungeon

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Nintendo 3DS Pokemon Super Mystery Dungeon Cover
Pokemon Super Mystery Dungeon - Nintendo 3DS Standard Edition (Renewed)

Embark on adventures with Nintendo Pokemon Mystery Dungeon for Nintendo 3DS. Befriend various Pokemon and journey through mysterious dungeons with them. You'll transform into a Pokemon and explore a world filled with these creatures. Choose your Pokemon and a partner from a selection of 20, including popular ones like Pikachu and Riolu. Interact with over 700 Pokemon as you work to save the world. This game offers a unique experience of being part of the Pokemon world, making it an exciting and immersive gameplay for fans.

What We Like
Various Pokemon to befriend
Explore mysterious dungeons
Interact with over 700 Pokemon
#TOP 4

Layton's Mystery Journey: Katrielle and the Millionaires' Conspiracy

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Layton's Mystery Journey: Katrielle and the Millionaires' Conspiracy Cover
LAYTON’S MYSTERY JOURNEY: Katrielle and the Millionaires' Conspiracy - Nintendo 3DS

Join Katrielle in solving the mystery of her father's disappearance in this latest entry into the PROFESSOR LAYTON series. Assemble clues and solve puzzles with an outside-the-box thinking to uncover secrets and crack the code. Celebrate 10 years of mystery solving with LAYTON'S MYSTERY JOURNEY.

What We Like
Interesting storyline
Challenging puzzles
Great for fans of the Professor Layton series
#TOP 5

Pokémon Mystery Dungeon: Gates to Infinity - 3DS (Renewed)

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Pokémon Mystery Dungeon: Gates to Infinity - 3DS (Renewed) Cover
Pokémon Mystery Dungeon: Gates to Infinity - 3DS (Renewed)

This Nintendo 3DS & 2DS game is an authentic Pokémon Mystery Dungeon: Gates to Infinity, which comes with only the cartridge and label, but they are in nice condition. The product has been fully tested and guaranteed.

What We Like
Authentic Pokémon game
Cartridge and label are in nice condition
Product is fully tested and guaranteed
#TOP 6

Etrian Mystery Dungeon - Nintendo 3DS

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Etrian Mystery Dungeon - Nintendo 3DS Cover
Etrian Mystery Dungeon - Nintendo 3DS

Etrian Mystery Dungeon is an exciting Nintendo 3DS game that offers infinite dungeons to explore. With the random map feature, the floor terrain changes every time you enter a dungeon, ensuring a unique experience every time. The game also allows for party customization, with up to 10 different class types to choose from. After your first journey as a Landsknecht, you can freely select your party of 4 and embark on thrilling adventures. The unique perspective in Etrian Mystery Dungeon adds a new level of challenge, requiring careful selection of party members and upgrading their abilities. Get ready to dive into a world full of mystery and excitement with Etrian Mystery Dungeon!

What We Like
Infinite dungeons
Party customization
Unique perspective
#TOP 7

Etrian Mystery Dungeon - Atlus

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Etrian Mystery Dungeon - Atlus Cover
Etrian Mystery Dungeon - Nintendo 3DS (Renewed)

Etrian Mystery Dungeon offers an exciting gaming experience with its randomly generated dungeons, ensuring that every adventure feels fresh and unique. You can customize your party of four from ten different classes, allowing you to tailor your team to your playstyle. This flexibility enhances your strategic options and keeps gameplay engaging. Additionally, the game’s combat system requires careful consideration when selecting characters and upgrading their skills, making every decision impactful. This attention to detail in both exploration and combat ensures that players remain invested in their journey through the dungeons.

What We Like
Randomly generated dungeons
Party customization options
Strategic combat system
Engaging gameplay experience
#TOP 8

Layton's Mystery Journey

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Layton's Mystery Journey Cover
Layton's Mystery Journey: Katrielle and the Millionaires' Conspiracy (Nintendo 3DS)

Layton's Mystery Journey: Katrielle and the Millionaires' Conspiracy is a puzzle game for Nintendo 3DS & 2DS. The game features Katrielle, Professor Layton's daughter, as the main character to solve the puzzles. The game includes more puzzles than any game in the Layton series so far and bonus puzzles will be available for download daily for one year after launch. The game is easy to pick up and play with Touch Screen-based gameplay that fans know and love. It is compatible with various consoles, including 3DS, 3DS XL, 2DS, New 3DS, New 3DS XL and New 2DS XL.

What We Like
Features more puzzles than any game in the Layton series so far
Bonus puzzles available for download daily for one year after launch
Easy to pick up and play with Touch Screen-based gameplay
#TOP 9

Metroid: Samus Returns - Nintendo 3DS

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Metroid: Samus Returns - Nintendo 3DS Cover
Metroid: Samus Returns - Nintendo 3DS

Metroid: Samus Returns is a complete remake of the classic Metroid II - Return of Samus, with engaging 3D visuals, a mysterious energy resource called “Aeion”, a powerful Melee counterattack, and 360-degree Free aim mode. It offers an immersive atmosphere and plenty of secrets to uncover, and is the longest 2D Metroid game with a run time of 20 hours. The gameplay is smooth and natural, and the Aeon abilities add a new dimension to the existing formula. However, the maps don't interconnect in the same way as other Metroid games, and the Melee mechanic is essential to progress.

What We Like
Engaging 3D visuals and atmospheric color palette
Plenty of secrets to uncover
Smooth and natural gameplay
Aeon abilities add a new dimension to the existing formula
Longest 2D Metroid game with a run time of 20 hours

Jake Hunter Detective Story: Ghost of The Dusk

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Jake Hunter Detective Story: Ghost of The Dusk Cover
Jake Hunter Detective Story: Ghost of The Dusk - Nintendo 3DS

Jake Hunter Detective Story: Ghost of The Dusk is a Nintendo 3DS game that offers hardboiled action and investigative gameplay. You will need to use all of your master detective skills to separate fact from fiction as you question suspects, search crime scenes, and zero in on inconsistencies to discover the truth. The game features all-new cases, original characters, and familiar friends. Additionally, you can discover passwords hidden throughout the game's world to unlock bonus features and side stories.

What We Like
Offers hardboiled action gameplay
Allows you to use your investigative instincts to solve mysteries
Features all-new cases, original characters, and familiar friends
Buying Guide Image

Frequently Asked Questions (FAQs)

1. Are 3DS games being discontinued?

Yes, the Nintendo eShop for the 3DS officially closed on March 27th, 2023, which means that new purchases and downloads are no longer available for the platform.

2. What was the last Nintendo 3DS game?

The last Nintendo 3DS game released in North America was Flying Axe, which came out in 2021. It is a game where players chop trees and need to sharpen their axe to prevent it from breaking.

3. Is Nintendo 3DS going away in 2023?

Yes, after March 27th, 2023, you will no longer be able to purchase or download new games, in-game content, demos, or free-to-play software from the 3DS or Wii U eShop. Adding funds to your account or redeeming download codes will also be disabled.

4. What is replacing 3DS?

While the 3DS is being phased out, there are rumors of a potential Switch Pro that could serve as a replacement for the 3DS line of systems. Nintendo has a history of introducing innovative handheld consoles.

5. Why is Nintendo shutting down 3DS?

Nintendo stated that the closure of the 3DS and Wii U eShop is part of the natural life cycle of the products. The popularity of the Switch console has overshadowed the 3DS and Wii U, leading to the decision to focus on newer platforms.

Editor's Notes

During our nintendo 3ds mystery game research, we found 16 nintendo 3ds mystery game products and shortlisted 10 quality products. We collected and analyzed 20,729 customer reviews through our big data system to write the nintendo 3ds mystery games list. We found that most customers choose nintendo 3ds mystery games with an average price of $53.16.

The nintendo 3ds mystery games are available for purchase. We have researched hundreds of brands and picked the top brands of nintendo 3ds mystery games, including Nintendo, Atlus, Aksys. The seller of top 1 product has received honest feedback from 1,041 consumers with an average rating of 4.8.

Written by
James Ryan Avatar

James Ryan is a young writer with a degree in journalism. He’s well-versed in topics such as literature, video games, and gaming devices. In his free time, he enjoys editing, playing games, exercising and photography.