Fanfic / Rain Code: New Game Plus

Rain Code: New Game Plus is a series of Master Detective Archives: Rain Code fanfictions written by MHJoker4Ever. This story covers the plot of the source material, but with the twist of the Master Detectives onboard the Amaterasu Express surviving the murder plot of Chapter 0.

This story assumes you have played the original game, so beware of unmarked spoilers from canon.

The series can be read here.

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This fanfiction has examples of:

• Abusive Parents: Karen's father forces his expectations onto his daughter, demanding that she get perfect results in her grades and her future career as an actress, and also controls which friends she hangs out with. He ultimately proves that he cares more about his reputation than his daughter's happiness and well-being, and the pressure he puts onto her contributes to her crime of passion against Aiko. He also slaps her when she confesses to the murders she committed just because it sullies his reputation.
• Abhorrent Admirer: Although it is ambiguous if Shinobu actually loves Yoshiko in a romantic way, Yoshiko definitely doesn't like how clingy Shinobu acts towards her and prefers to avoid her. When Shinobu sees Yoshiko and tries to approach her while she's keeping an eye on Desuhiko, Yoshiko pales and immediately runs away from her.
• A-Cup Angst: Pucci gets infuriated at the sight of Shinigami's large breasts, desperately trying to convince herself they're not real. Shinigami certainly enjoys rubbing this in her face and making fun of Pucci's smaller chest.
• Adaptational Dumbass: In the canon game’s Chapter 0, the Peacekeepers prepared a spare train car identical to the first car at the station so the Amaterasu Express would connect to it and thus make Yuma think he was passing through the original first car. Here, they do no such thing, leading Yuma and Pucci to exit out of the second car and notice Car 1 is missing. Yuma and Pucci even lampshade this, with Pucci noting that the Peacekeepers were rather arrogant to think they can just leave out an important detail and keep the Master Detectives from noticing anything suspicious.
• Adaptational Gender Identity: While Halara's physical sex and gender identity in canon are deliberately kept ambiguous, here, the narrative and the characters refer to Halara as female.
• Adaptational Context Change: In canon, Kurumi Wendy is the one who enlists Yuma's aid in investigating Aiko's death on the day of the school play, and she also sees Yuma go into disguise and keeps his secret safe for the sake of the investigation. Here, Kurane enlists Yuma instead days before the school play and Kurumi first meets Yuma while he's in disguise, so she's initially unaware that Yuma isn't a girl and is also one of the detectives she admires so much. She initially meets with "Yumi" to politely ask "her" to stop the investigation out of concern for "her" safety, and only agrees otherwise when Yuma provides incentive.
• Adaptational Heroism: Downplayed. Kurane, one of the killers of Chapter 2, starts to have reservations about murdering Karen since she doesn't want her friends to get in trouble. When she witnesses Yuma go out of his way to prove the innocence of her friend Mei, she decides to hire him to investigate Aiko's death in the hopes that he can expose Karen as Aiko's killer before the day of the play and thus avoid any bloodshed. However, when Karen's death seemingly does occur (even if Kurane didn't take part in it), she reluctantly puts the blame on the disguised Yuma in order to spare her friends from getting investigated and potentially arrested by the Peacekeepers. But when Yuma disguises himself as a Peacekeeper and offers to have all the blame be put on "Yumi Cyclone", Kurane instead tells the "Peacekeeper" that she's responsible for Karen's death so that Yuma, Yoshiko, and Waruna would be spared, unable to bring herself throw her friends or any innocent people under the bus. Following the events of the chapter and getting Spared by the Adaptation, Kurane, alongside Yoshiko and Waruna, feel remorse for their actions and decide to atone, with Kurane being the most determined to make amends with Yuma.
• Adaptational Karma: Desuhiko faces no consequences in canon for impersonating Hana and getting her stalked by the music teacher because of his flirtation with the latter. Here, Desuhiko has to solve the stalker case after hearing from Hana about her fears regarding both her impostor and stalker. After deducing the stalker's identity, he is forced to confess how he impersonated Hana and gets dragged back to the Nocturnal Detective Agency to be lectured by Yakou for his actions.
• Adaptational Sympathy: This story gives more insight into Karen's backstory and feelings towards Aiko. Even though she was annoyed by her insistence on helping her, Karen never actually hated her and respected her talents as an actress. When she kills her in an act of impulse after all the stress of fulfilling her father's expectations finally boiled to the surface, Karen felt guilty for it but chose to bottle up her feelings because she was afraid of the scorn she would receive if word got out. But the more people kept digging into what happened to Aiko, the more pressured Karen felt, and learning that Yoshiko and Waruna intend to poison her finally led her to decide to fake her death so she can get out of Kanai Ward.
• Adaptation Distillation: The events of Chapter 1 in canon are only referenced in the story, with only events in the aftermath resulting from the case being shown instead before Chapter 2.
• Adaptation Expansion:
  • Yuma's time investigating Aetheria Academy is changed to 3 days instead of a single day like in canon. Because of this, Yuma gets to spend more time learning about the students during his investigation, including Kurane and her friends.
  • Aiko's characterization is fleshed out in the flashbacks of Chapter 2, showing how she tried to help her friends in the Theater Club with their respective problems.
• Adaptation Origin Connection: Zange here is revealed to be Yakou's former mentor when the latter was training to be a detective, whereas no such relationship is ever mentioned in canon due to Zange being killed off in Chapter 0.
• All for Nothing: Yuma convinces Karen's soul in the Mystery Labyrinth to confess to her crimes in the real world, promising that he will do everything he can to help her live so she can atone for her actions, and her return to her true self destroys the Mystery Labyrinth without having to kill her. Sadly, Yomi decides to take advantage of this to set Karen and her father up to a public execution as an excuse to get the family assets. Yuma is unable to help despite his best efforts and is left devastated after being Forced to Watch her execution on live television.
• Ascended Extra:
  • In canon, the Master Detectives Yuma meets on the Amaterasu Express are all killed by the hitman impersonating Zilch before they reach Kanai Ward. Here, they survive thanks to Yuma's role as a Spanner in the Works and manage to make it to Kanai Ward, allowing them to become major characters alongside the Master Detectives at the Nocturnal Detective Agency.
    • To a lesser extent, the real Zilch Alexander ends up getting a bigger role in the mystery of Chapter 0 despite still being a Posthumous Character, as his corpse is used by the hitman posing as him to stage a fake murder. In canon, it's mentioned that the real Zilch's corpse is hidden in the spare first car at the Kanai Ward station, but neither Yuma nor the player ever gets to see the body.
  • The named Peacekeepers get more prominence here than in canon. Swaink is mentioned getting involved in incidents involving the Master Detectives from the Amaterasu Express, and Seth becomes a major character after Martina convinces Yomi to spare his life and demote him instead of executing him.
  • Although Kurane was already important in Chapter 2 due to being one of the killers in canon, here, she actually becomes a major character and ally of Yuma as she enlists him to investigate Aiko's death. Yoshiko and Waruna also become major supporting characters after the events of Chapter 2.
  • Karen goes from the victim of Chapter 2 to the culprit, having killed a student named Ayako in order to fake her death and get out of Kanai Ward.
  • One of Yakou's former co-workers, Souta Crawford (who was introduced in the DLC), makes his appearance in the story and will become an important character later on.
• The Atoner: While Yoshiko, Waruna, and Kurane all go through a Heel Realization following the events of their failed murder attempt and their attempts to pin the blame on Yuma, Kurane is the most guilt-ridden by what happened and wants to make amends for what she put him through.
• Attractive Bent-Gender: Everyone who sees Yuma's female disguise are utterly stunned by how cute he looks as Yumi Cyclone. Kurane and Pucci are flustered and blushing red at the first sight of Yuma in disguise, Yoshiko has to pause in her conversation with Kurane about Yuma just to clarify if he's really a guy (admitting that his disguise is so convincing that she never would have suspected otherwise), and Waruna is still having trouble believing that Yuma is actually a guy.
  Waruna: No boy should look that pretty. You sure that Yuma’s actually a guy?
  Kurumi: [nodding] Mmhm. I’m not complaining, per se… But Yumi-chan was adorable~…
• Awesomeness by Analysis: Although Pucci doesn't remember her time in the Mystery Labyrinth, she does deduce that Yuma had something to do with the Fake Zilch's death and that the circumstances are outside his control.
• Cassandra Truth: When the Priest is channeled by Melami so the Nun and the Servant can say their goodbyes, the Priest claims he and Elizabeth were Devoured by the Horde and he hopes that Matthew and Jason got at least some of the survivors to safety. When the confused Elizabeth and Matthew tell him he died of a heart attack and he confessed to being the Nail Man and killed 3 people, the Priest shows genuine shock and confusion, swearing that he’s not a murderer and he really did die in brutal agony. Everybody assumes that something went wrong with the channeling, and it messed with his recent memories, but what they don’t know at the time is that the Priest is telling the truth. The Priest being channeled is actually the original and not the homunculus who became the Nail Man.
• Cathartic Crying: After Yuma makes it clear that he still cares for Kurane despite her actions during the Aetheria Academy case and still wants to be her friend, Kurane can only hug Yuma and cry her heart out.
• Class Princess: Downplayed. Aiko was shown to be well-liked by many at Aetheria Academy for her kindness and willingness to help people, which allowed her to befriend almost anyone at school. Even Karen couldn't bring herself to dislike Aiko, despite finding her attempts to help her annoying, and this just made it all the more tragic when she killed her in the heat of the moment. It's downplayed because it's shown that not everyone liked Aiko and some were even jealous, which led to some girls talking ill about her behind her back. It's also shown that while Aiko is a good person, she also had her personal flaws and a hidden selfish streak, as she once feigned illness just to take a break from school.
• Clingy Jealous Girl: Pucci doesn't like it when other girls get too close to Yuma, though she would never admit it.
• A Day in the Limelight: Chapter 2.5: The Aftercredits has 10 chapters that each revolve around a detective at the Nocturnal Detective Agency.
  • The first chapter revolves around Yakou's reminiscing about his late wife Serika and reveals to the reader in advance that he intends to kill Dr. Huesca in revenge for supposedly killing her. It also revolves around his attempts to be a Father to His Men as he goes out of his way to comfort Yuma after his failure to save Karen and has Kurane promise to watch over Yuma and make sure he doesn't get himself into too much trouble.
  • The second chapter has Desuhiko solve the case of Hana's Stalker with a Crush in Yuma's place, while also having Yoshiko, Waruna, and Kurumi watch over him so he doesn't get into any perverted mischief.
• Crime of Passion: Karen's history and crime of passion against Aiko are expanded on as part of her Adaptational Sympathy treatment. Karen felt pressured living up to her abusive father's expectations, which led her to bottle up her emotions. Aiko could sense Karen was feeling troubled and wanted to help her, and though Karen felt annoyed by her persistence, she could never bring herself to hate Aiko. On the night of Aiko's death, Karen would meet Aiko in the back of the school yard where Aiko promised she would help her get through her troubles and lends her hairpin to her as proof of this. This unfortunately caused all of Karen's repressed frustrations to finally boil to the surface and led her to kill Aiko in a fit of blind rage. Karen is utterly horrified and regretful of what she's done, but she ends up covering up the incident due to her fear of being scorned. But the more people kept trying to dig in to what happened, the more pressured Karen felt, which led her to plot to fake her death after discovering she's being targeted for murder just so she can finally leave her life as Karen behind.
• Death by Genre Savviness: The hitman impersonating Zilch takes and hides the real Zilch's corpse in the first train car's main control room to use as a contingency plan in the event he failed to drug all the Master Detectives on-board, which comes to pass when Pucci finds out through her Forte that Yuma has been drugged. After drugging Aphex, the hitman leaves Zilch's body in the second car and sets it on fire in order to burn the corpse beyond recognition and hopefully destroy any evidence that could link him to the crime while he hides in the detached first car going on a separate track. While the hitman succeeds in faking his death, he still ends up leaving tons of evidence, which combined with the Peacekeepers' incompetence, allows Yuma and Pucci to uncover him as the culprit in the Mystery Labyrinth. Justified, as the hitman had no way of knowing about Shinigami and her power to kill him through the Mystery Labyrinth.
• Decomposite Character: Although Yuma is still the main protagonist, the other Master Detectives end up doing the sidequests in his place, such as Pucci helping the Servant learn that true strength comes from heart and Desuhiko solving Hana's stalker case.
• Deconstructed Character Archetype: Desuhiko's Casanova Wannabe tendencies are deconstructed in this story by showing how much he makes ladies uncomfortable with his attempts to flirt with them. He even goes out of his way to sneak into Aetheria Academy after the murder case has been solved just to get close to girls, which gets him in trouble more than once due to security being upgraded as well as Waruna and Yoshiko being on lookout duty. Melami and Kurumi gently criticize his behavior by telling him how he tries too hard to get girls to like him and his attempts to flirt with multiple women would potentially shoot down any chance of getting a genuinely romantic relationship.
• Dies Differently in Adaptation: Karen avoids being poisoned here, but when she confesses her crimes, Yomi has Karen and her father executed on live television by being beaten to death by Dominic Fulltank.
• Distracted by the Sexy: Melami invokes and exploits this trope when she's dealing with the male Peacekeepers, partially stripping to distract them and convince them to let her go whenever they capture her.
• Dreadful Musician: Implied. When Desuhiko announces a song he’s going to play on his guitar, everyone at the Nocturnal Detective Agency (except for Fubuki, who gets excited at most things) doesn’t seem particularly enthused about it. Halara, Vivia, and Zange are completely stoic, Melami and Aphex cringe slightly, Yuma looks nervous, and Pucci especially pales at the sight of the instrument and immediately dons her noise-canceling headphones. Yakou’s bursts into the room before Desuhiko can play though.
• Easily Forgiven: Deconstructed. Although Yuma does forgive Yoshiko, Waruna, and Kurane for trying to pin their murder attempt on him and doesn't press any charges against them for trying to go through with the murder, the girls don't feel like they deserve forgiveness from him. Yoshiko and Waruna especially feel the most uncomfortable with how quickly they're forgiven and want to actually earn that forgiveness.
• Even Evil Can Be Loved: Even though the Nun and the Servant find out that Father Elijah is the Nail Man, they still care for him as the man who took care of them, to the point that they ask Melami to channel his soul so they can say their goodbyes to him and call him out for the murders he committed.
• Everyone Has Standards: Although Yoshiko, Waruna, and Kurane want revenge on Karen for killing Aiko, even going out of their way to plot murder when exposing her as a killer doesn’t work, they are all just as horrified as everyone else to see Karen beaten to death by Dominic on live television. Despite wanting Karen to be punished, even they believe that this is too cruel for her.
• Faking the Dead:
  • The hitman impersonating Zilch is forced to resort to this after Yuma accidentally foils his trap by passing out in front of the other Master Detectives. After drugging Aphex into unconsciousness, the hitman leaves the real Zilch’s corpse in Car 2 and sets the room on fire to burn the body beyond recognition before he goes to Car 1 and detach it from the rest of the train. Since he’s currently traveling on another track, Pucci is unable to hear his heartbeat with her Forte, thus making his faked death all the more convincing.
  • Karen catches on to Yoshiko and Waruna’s plan to poison her, so she decides to exploit this to fake her death. Swapping the poisoned and marked cup with a cup she marked and stole from the props, Karen discreetly placed a blood pack into her mouth after drinking from her cup while pretending to feel the poison take effect, then burst the blood pack in her mouth to create the illusion she was poisoned. After the Peacekeepers cleared out the theater hall, Karen had the Peacekeepers exchange her outfit with the recently killed Ayako and clean up the blood on her. Karen would place a wig similar to her hairstyle on Ayako’s body while wearing a black wig to complete her disguise.
• Fallen Hero: From what little we see of the original Elijah, he was a genuinely kind priest who would never even consider committing murder. His homunculus, unknowingly replacing the original and living his life, likely succumbed to cynicism after living for years in the corrupt city as he decided to become the Nail Man and appeal to the people's wish to kill the corrupt.
• Five-Second Foreshadowing: We get a hint that the Priest channeled by Melami is not the same Priest who became the Nail Man when he looks around the church and shows surprise that it's been restored and asks if what he saw was a dream.
• Foreshadowing:
  • While the plot twist about the Homunculi and the Blank Week Mystery isn't revealed yet at this point in the story, it does end up getting more foreshadowing when Elizabeth and Matthew (The Nun and the Servant respectively) ask Melami to channel the soul of Father Elijah so they can say their goodbyes to him and call him out for the murders he committed as the Nail Man. However, everyone ends up confused when the priest doesn't remember killing anyone and seems to recall himself and Elizabeth dying via being Devoured by the Horde instead. This is because Melami is channeling the soul of the original priest and not the soul of the homunculus that became the Nail Man.
    • The above foreshadowing also leads to another bit of foreshadowing about the homunculi in Chapter 2. When Yuma borrows Melami's Spiritism Forte, he tries to channel Karen's spirit, but gets no results at all. Yuma realizes in the Mystery Labyrinth that Karen faked her death and concludes that's why the channeling failed. However, considering that Melami (unknowingly) channeled the soul of the original Priest Elijah instead of his homunculus, it's likely that the original Karen never wore such clothes in life. If that had been the case, the original Karen would have been channeled by Yuma and immediately set off alarm bells about the homunculi and the Blank Week Mystery.
• Heartfelt Apology: Yoshiko gives one to Kurane after her Heel Realization following Karen's survival and decision to turn herself in, admitting she was wrong to ever come up with the idea to murder Karen and drag her friends down this path.
• Heel–Face Door-Slam: A rather heartbreaking example. Karen regrets killing Aiko in an act of impulsive anger but bottles up her feelings because she's afraid of being scorned. Yuma convinces her soul to confess in the real world, so she won't have to die in the Mystery Labyrinth. Unfortunately, Yomi decides to take advantage of this by sentencing Karen and her father to execution, and Karen can only plead for mercy as she's being dragged off, knowing she'll never have the chance to atone for her crimes.
• Hoist by His Own Petard: Although it's not completely his fault due to the Peacekeepers' incompetence, the Fake Zilch's contingency plan still ends up doing him in due to leaving a ton of evidence for Yuma to find and make the connection to him. The decisive piece of evidence that allows Yuma to prove it's him comes from the small shards of glass that came from the real Zilch's glasses, which were left behind in the first car while the impostor was moving the real Zilch's body, with Pucci able to recall them in the Mystery Labyrinth. The Fake Zilch was in such a hurry that he failed to notice the small shards of glass left behind as he moved the real Zilch's corpse and leaving them unattended ended up sealing his fate.
• Impersonation-Exclusive Character: Ayako Fuwa is a student of Aetheria Academy who works tirelessly to design the set for the theater club. She was Killed Offscreen by Karen as part of her plan to fake her death, with Karen impersonating her after the Peacekeepers clear everyone out of the theater hall and dress up Ayako’s body as Karen’s.
• In Spite of a Nail:
  • Even though the Master Detectives on-board the Amaterasu Express (except for the real Zilch, who was already killed by the hitman before everyone got on the train) are saved from the Fake Zilch's murder attempt, Yuma still has to go into the Mystery Labyrinth for the first time, if only to prove everyone's innocence when they're accused of killing Zilch. The only difference here is that he has Pucci to accompany him. The Fake Zilch still has his soul reaped by Shinigami after Yuma reaches the truth in the Mystery Labyrinth.
  • Even though it's Kurane who ends up enlisting Yuma to investigate Aiko's death, Yuma still meets and befriends Kurumi Wendy as they both agree to investigate Aiko's death together. After the case is resolved, she tells Yuma (along with Yoshiko, Waruna, and Kurane, who are accompanying her and Yuma) about Amaterasu's experiments into creating a homunculus.
  • Even though Karen avoids her death at the hands of Aiko's friends and also gets spared from having her soul reaped by Shinigami, she still ends up dying, this time by being executed by Yomi.
  • Even though Melami impersonates Hana during the case to solve Aiko's death at Aetheria Academy, Desuhiko still impersonates the teacher and his actions while in disguise lead to the real Hana being stalked by the music teacher. The only difference is that this happens after the case is solved and Desuhiko has to clean up his mess by solving the case.
• Kindhearted Cat Lover: It turns out that Halara is not the only one who likes cats or likes to look at photos of them. Pucci also has photos of cats that she gets embarrassed about when Halara finds one that has been dropped out of her pocket. Fubuki also takes a kindle of kittens to the sub, much to Yakou’s dismay.
• Kick the Dog: Yomi sentencing Karen and her father to a cruel and unusual execution was already horrible enough, but he goes out of his way to televise the execution to all of Kanai Ward and sadistically thank the Nocturnal Detective Agency for finding out the truth just to turn the city against them, as if to say that it’s all the detectives’ fault that the citizens have to watch such a horrific sight. Yuma, who was trying to vouch for Karen to have a fair and humane punishment, is understandably devastated that he failed to save Karen like he promised.
• Late-Arrival Spoiler: The story assumes you are familiar with the source material, so it doesn't bother to hide the identities of the culprits from canon^note Chapter 0 already lets us know ahead of time that the hitman impersonating Zilch killed the Master Detectives onboard the Amaterasu Express in canon, Chapter 1 reveals the killers to be the Priest and the Worshipper even though the events of the Nail Man are only referenced, and Chapter 2 lets us know that Yoshiko, Waruna, and Kurane intend to poison Karen to avenge Aiko's death. or the plot twists that will come later^note Yakou's Day in the Limelight chapter reveals that he intends to kill Dr. Huesca for supposedly killing his wife.. It's the how plot goes into a different direction that ends up being the real surprises.
• Lethal Chef: Although she doesn't take it as severely as Yakou does, even Pucci can't hide from Yuma that his cooking is terrible, though Pucci blames it on Yuma's memory loss.
• Leeroy Jenkins: When Aphex sees Iruka with a gun, he gets confrontational with her despite Pucci's warnings, and this leads both of them to get chased off by Iruka as she opens fire on them. This leads Yakou to ban Aphex from going to Dohya District.
• Logical Weakness: Aphex and Pucci can detect living people with their Fortes within a 50- and 500-meter radius respectively. The hitman posing as Zilch has to exploit their weaknesses in order to put his contingency plan in motion, knowing that they'll be using their Fortes to check on everyone's status on the train occasionally. The hitman first lures Aphex into a room to drug him since he knows that Aphex's Life Detection is pinpoint accurate but does not kill him since he knows that Pucci will sense through her Forte that someone has been killed. After the hitman returns the unconscious Aphex to his room, he is able to fake his own death by leaving the real Zilch’s corpse in Car 2, set the room ablaze so the body will be burned beyond recognition, and go onto Car 1 and detach it from rest of the train before going on a separate track. Since the train everyone else is on went into a tunnel far enough away from the still moving Car 1, Pucci is unable to hear the hitman’s heartbeat with her Forte. It’s only when Car 1 attaches to the back of the train that Pucci and Aphex are able to detect his presence, but since they believe "Zilch" is dead, they are unable to identify the sixth individual that just appeared on the train.
• Morally Superior Copy: Inverted. The priest who gets channeled by Melami (who unbeknownst to everyone, is actually the original priest and not the homunculus created from his blood) shows genuine shock and confusion at being called a murderer and states he would never stoop to murder. Everyone present is understandably confused.
• My God, What Have I Done?:
  • When Melami hears from Swaink that the coffee she served Yuma was drugged, she's utterly horrified.
  • Karen is horrified when she kills Aiko in a Moment of Weakness, but she ends up framing it as a suicide because she's afraid of the scorn she'll receive and ends up bottling up her emotions even further.
• Named by the Adaptation:
  • The Nun, the Servant, the Worshipper, and the Priest are given the names Elizabeth, Matthew, Jason, and Elijah respectively in this story.
  • Aiko, Kurane, Yoshiko, Waruna, and Karen are given the surnames Gracewill, Ravencroft, Nocturne, Stormbreaker, and Stromwell respectively.
  • Some of the unnamed students of Aetheria Academy are given names in this story. In particular, there is Kari the props manager, Kotomi the production manager (the student who alerted everyone to Karen's death), and Miiko the girl who asked Kurumi to help her backstage before the performance.
  • Yakou’s late wife is given the name Serika.
• Nice Mean And In Between: Kurumi, Waruna, and Yoshiko have this dynamic respectively while they're watching Desuhiko during his investigation of Miss Hana's stalker. Kurumi is the most patient with him and willing to give him the benefit of the doubt, Waruna is most skeptical of his innocence and tends to jab him whenever he does or says something stupid, and Yoshiko is also skeptical of Desuhiko but willing to give him the chance to investigate, though she does take advantage of the brief moment she's separated from the group to call Halara and Melami over to deal with him during the investigation.
• Not Me This Time: When Desuhiko tries to explain that he has permission to be at Aetheria Academy to investigate a stalker case, Waruna and Yoshiko don’t believe him initially since he has trespassed onto Aetheria Academy grounds time and again, and Waruna even believes he is the stalker. Kurumi is the only one willing to give him the benefit of the doubt, and after she confirms with Miss Hana about Desuhiko’s status, Yoshiko reluctantly decides to let him investigate while he’s under their watchful eye. While Waruna is the most opposed to this decision, Yoshiko immediately points out that if Desuhiko really is the stalker, it would be stupid of him to get permission from Hana to be on the grounds since they’ll be keeping an eye on him regardless.
• Obfuscating Postmortem Wounds: As part of his back-up plan to frame the Master Detectives for murder, the Fake Zilch leaves the real Zilch Alexander's corpse in Car 2 and sets it on fire to burn the body beyond recognition, both to fake his death and to hide the victim's real cause of death. The Peacekeepers report to Swaink that Zilch was burned to death, but Yuma becomes suspicious of the whole thing due to remembering that the body had a knife stabbed in the chest, which allows him to discover in the Mystery Labyrinth that the victim was actually stabbed to death and that the body on the train isn't actually the Zilch they know.
• O.O.C. Is Serious Business:
  • Played for Laughs with Yoshiko. When Waruna tells Melami and Yuma that Yoshiko would have given Desuhiko a stern talking to and stop Waruna from doing anything, Yoshiko tells her that she'll make an exception with Desuhiko and leave him to Waruna, after having to put up with so many problems with the other girls and Desuhiko's antic with them.
  • Played more seriously with Yomi Hellsmile following the events of Karen's confession. Martina notes that the fact that Yomi is acting quiet and not throwing a tantrum following the Peacekeeper's ineptitude with the case at Aetheria Academy means that Yomi is planning something horrifying, and Martina can only brace herself for what that plan is.
  • Aiko's hairpin was noted to be her prized possession since it was a gift from her father, and her friends state she would never give it away. Aiko shows just how much she wanted to help Karen make it through her troubles by lending her hairpin to her, an act that unfortunately leads to her death when all of Karen's repressed frustration causes her to kill Aiko in the heat of the moment.
• Out-of-Character Alert: While investigating Karen's apparent death on the stage, Melami and Yuma disguise themselves as Martini and a masked Peacekeeper respectively as they come across what appears to be Seth consoling a student named Ayako (who unbeknownst to them, is actually Karen in disguise). Seth sees through the disguises immediately because Martina would never stop to "verify" if a girl was safe due to her confidence in a case. He deliberately doesn't say anything however out of respect for the detectives and wants to see if they will leave or not.
• Open Mouth, Insert Foot: When Desuhiko is forced to admit that he impersonated Miss Hana and that he was the one who called music teacher lovely, he nervously tries to tell her not to stalk Hana anymore… unless she permits it. Waruna facepalms, Halara massages her brow in disapproval, and Yoshiko and Melami sport a Grin of Rage.
• Pervert Revenge Mode: Waruna and Yoshiko both set up a patrol around Aetheria Academy to keep Desuhiko out whenever he sneaks into the school. Waruna in particular is quite eager to hit him in revenge for his perverted antics.
• Pragmatic Villainy: Martina convinces Yomi to demote Seth instead of executing him by pointing out they'll need every Peacekeeper available to fight the Master Detectives. Yomi also decides to spare Martina instead of crushing her into a cube, though the fact that he still gloats about his original intentions for her understandably horrifies Martina.
• Prized Possession Giveaway: Aiko's hairpin was a gift from her father and her friends note she would never give it away, which makes it suspicious when a figure drops it on the way out. Karen reveals in the Mystery Labyrinth that Aiko wanted to help her so much that she decided to lend the hairpin to let her know she always has her back, and she can return it to her when life at home is stabilized, but it unfortunately caused all of Karen's repressed feelings to boil to the surface and led her to kill Aiko in the heat of the moment. She held onto it ever since, unwilling to throw away the only thing left of the person who tried to help her.
• Properly Paranoid: Zange finds it rather peculiar for the people of Kanai Ward to be so addicted to the meat buns and elects to investigate it. Some of the other Master Detectives, such as Desuhiko and Aphex, doubt that the meat buns will provide any important clues, but we on the other hand know that Zange is right to be suspicious of the meat buns.
• Point of Divergence:
  • The plot starts go in a different direction when Yuma passes out in front of the Master Detectives on the Amaterasu Express, which ends up saving them from the Fake Zilch's murder plot and allows them to reach Kanai Ward alive.
  • The events of Chapter 2 also play out differently when Kurane witnesses Yuma go out of his way to prove the innocence of the former's friend Mei of a pickpocket crime. She blackmails him into investigating the death of Aiko 6 months prior in the hopes he can expose Karen as the killer before the day of the school play, so she and her friends won't become murderers.
• Poisoned Chalice Switcheroo: Unlike in canon, Karen discovers ahead of time that Yoshiko and Waruna intend to poison her, so she decides to use it to her advantage to fake her death. Stealing an extra glass prop of her own and marking it, Karen swaps it out with the marked cup Yoshiko poisoned, then discreetly places a blood pack into her mouth after drinking from her cup and bursts it to create the illusion she was successfully poisoned.
• Repression Never Ends Well: Karen felt pressured to live up to her father's expectations but chose to keep her feelings hidden. She also feels guilty about killing Aiko, but she bottles up her feelings because she's afraid of the scorn she'll receive if word got out. It turns out that when Aiko tried to help her, all of Karen's repressed frustration finally boiled to the surface and led her to kill Aiko in the heat of the moment. As more people kept trying to dig into what happened, it put more pressure on Karen until she finally decided to murder Ayako and fake her death just to get out of Kanai Ward.
• Right for the Wrong Reasons: Yuma and the Master Detectives come across a charred corpse on the Amaterasu Express and conclude that it's Zilch's due to the body wearing the latter's hat. It is indeed Zilch Alexander's body; it's just that the Zilch they met on the train is actually a hitman who killed and replaced him.
• Ripple-Effect-Proof Memory: Because of her spiritual affinity, Melami not only manages to keep her memories from Chapter 2's case in the Mystery Labyrinth, but also take her memories of what happened there into the real world.
• Sadist Teacher: Played for Laughs. Zange, who was Yakou’s mentor as a Detective, decides to give a remedial Training from Hell to punish Yakou for treating Yuma as a housekeeper.
• Samaritan Relationship Starter: Pucci, having acted as The Spock throughout her career as a Master Detective, develops an interest in Yuma after he goes out of his way to pick up her dropped Detective Deed for her. This leads to a case of What Is This Feeling? as she becomes protective of Yuma.
• Secret Diary: Yuma receives Karen's diary while disguised as Martina from one of the Peacekeepers, with Yuma discovering Karen's thoughts towards and her grudging but sincere respect towards Aiko as well as a torn photograph of the latter. Yuma would give the diary to Yoshiko, Waruna, and Kurane so they'll still have something to remember Aiko from.
• Secret Test of Character: After Kurane puts all the blame on Yuma so the Peacekeepers won't go after her friends, Yuma confronts her while disguised as a Peacekeeper in order to see if she's truly betrayed him. He offers to have all the blame put on "Yumi Cyclone" in exchange for her testimony, but Kurane ultimately can't bring herself to throw Yuma under the bus to save her friends and instead puts the blame on herself.
• Serious Business: Pucci lampshades how the students of Aetheria Academy take Drama Club way too seriously.
• Sobriquet Sex Switch: While disguised as a girl, Yuma goes by "Yumi Cyclone".
• Spanner in the Works: Yuma, instead of going to the restroom like he does in canon, ends up passing out in front of the Master Detectives. Pucci realizes that he's been drugged and insists on watching over him in her room, with the Master Detectives becoming hypervigilant now that they know there is something amiss. The fake Zilch, unable to drug everyone and make them vulnerable like he originally planned, is forced to go for his contingency plan and fake his death, placing the real Zilch's body (which has been charred beyond recognition) in Car 2 and set fire to Car 4 in the hopes of killing some of the Master Detectives or, failing that, frame them all for his death. If Yuma hadn't used the Mystery Labyrinth and Chief Yakou hadn't interfered following that, they would have all been arrested by the Peacekeepers on the spot.
• Spared by the Adaptation:
  • The Master Detectives on board the Amaterasu Express are saved from the Fake Zilch's murder plot thanks to Yuma being a Spanner in the Works.
  • In canon, Seth Burroughs was last seen being sentenced to execution by Yomi, but it's left ambiguous if he's dead or not. Here, he is still alive due to Martina convincing Yomi to demote him instead by pointing out that they'll need as many Peacekeepers as possible to fight against the Master Detectives.
  • Yoshiko, Waruna, and Kurane all get to live in this story, since their murder attempt on Karen failed.
  • Subverted with Karen. Although she manages to avoid being murdered by Aiko's friends and Yuma convinces her to confess in the real world and turn herself in to the Peacekeepers, Yomi decides to execute her and her father in order to salvage his reputation and get ahold of the Stromwell family assets.
• Sugar-and-Ice Personality: Pucci tends to be either abrasive or coldly professional when speaking to people. When interacting with Yuma however, she shows a more vulnerable and sweet side of her personality.
• Suspiciously Specific Denial: A Running Gag has the narrative describe the characters' feelings this way, such as the narrative describing Pucci's interest in Yuma as being somehow significant and not because of his act of kindness towards her, or when Yuma described the Chief's punishment as the Chief needing to pull his weight and not because he feels petty.
• Sympathy for the Devil: Although Yuma admits that he can't forgive Karen for her actions, he can't hate her at all, since she's a teenager living in a corrupt city that forced their expectations on her and put her through a lot of misery. Because of this, Yuma convinces her soul to confess in the real world and tries to vouch for a humane and fair punishment for her, but it sadly ends up for naught when Yomi sentences Karen to execution.
• This Is Gonna Suck:
  • Played for Laughs when Desuhiko, knowing that Melami doesn't like wearing boring and unfashionable clothes, nervously tells her about the request from the Nun to channel the Priest's soul. Melami acts eerily calm about the request, but Desuhiko can tell she's fuming about the whole thing with a forced smile as she reluctantly changes into Father Elijah' robes, knowing that she'll be asking for payment from him later.
  • Played much more seriously when Martina acts nervous about Yomi's eerily calm behavior following Karen's confession, knowing that he's planning something vicious.
• Violently Protective Girlfriend: She's not actually Yuma's girlfriend, but Pucci tends to look out for Yuma's wellbeing and gets angry when someone is threatening him. She (ineffectually) starts hitting Shinigami whenever she harms Yuma in some way in the Mystery Labyrinth and tends to get very defensive whenever someone is talking down to Yuma.
• Undying Loyalty: Seth Burroughs is loyal to Martina rather than Yomi since she convinced Yomi to spare his life.
• Warts and All: Downplayed. Aiko's kindness and desire to help others is sincere, though Karen suspected she had a hidden selfish streak. Aiko did indeed have personal flaws, but she was never a bad person in the slightest (she once faked an illness just to get out of school for a week and relax, but she still went out of her way to make it up to everyone). Karen was the only person to see this selfish side of her.
• "Well Done, Son" Guy: Karen tried to live up to her father's expectations by getting good grades and learning to be a good actress at Aetheria Academy, at the expense of bottling up her emotions. Nothing she did ever felt good enough and it only made things worse.
• What the Hell, Hero?: During Yakou's Day in the Limelight chapter, Yoshiko confronts Yuma about Vivia having a syringe on his person and demands to know why the WDO would have someone like him in their ranks. Yuma and Yakou, not knowing about this, are left at a loss for words. When Yuma tries to find the chief, Yakou immediately hightails it out of there due to not wanting be asked a question he doesn't have an answer to.
• What You Are in the Dark: Invoked by Yuma while he's disguised as a Peacekeeper in order to test Kurane's moral character after she accuses him of being Karen's killer. He offers to put all the blame on "Yumi Cyclone" in exchange for Kurane's testimony, promising that this won't be traced back to her. Unable to bring herself to abandon Yuma to save her friends, Kurane instead tells the "Peacekeeper" that she's responsible for killing Karen and remains resolute in her word.