The plot is positively drowning in subtle hints towards the game's central twists. There are many times where characters will go places, ask questions, and get no new information, giving the impression that the game is spinning its wheels, but these scenes invariably contain clues as to what's actually going on.
Regarding the true chronological timeline of the game's events:
- In Ryuki's storyline, at one point he attempts to capture a suspect who may be the killer in the underground cathedral beneath Naix headquarters, but the suspect manages to escape. The very next scene, we are at ABIS where Boss is severely chewing Ryuki out for his mistake and saying that her superiors were seriously considering firing him and that she was able to talk them down to demotion to a beat cop. At first glance, this all seems rather excessive for letting a suspect get away, even a murder suspect. But once the true timeline of events is revealed, you can see that the chewing out and demotion isn't for letting a suspect get away, it's for nearly murdering a civilian during a mental episode (an event we learn about during Mizuki's (Bibi's) segment), which he did upon seeing a theme park mascot putting up balloons after learning that the killer was leaving balloons with clues around town.
- As a bonus, if you inspect the balloons in Boss' office, Ryuki's first thoughts are "Tch..." clearly acting as a sour reminder of his failure.
- Amame attempts to explain her current depressive episode as her having lost big in pachinko. At this point in the story, Amame should be under the legal gambling age and yet Ryuki, a by-the-book police officer, doesn't question it. Tama as well cited a specific article in an earlier scene when pointing out that Amame's late night hours at Sunfish Pocket are illegal, and yet here she doesn't call attention to Amame's growing list of illegal activities either. This scene is actually taking place after the timeskip, where Amame is 24 and thus the prospect of her gambling doesn't raise any eyebrows.
- Some things are immediately off in Gen's Somnium. While a few can be initially dismissed as Somniums not needing to match up perfectly with reality, they become more understandable once the truth is revealed.
- Ota as his younger self appears which doesn't make much sense considering Ota has a new look post-timeskip. That is, it wouldn't make much sense unless the chapter is actually taking place 6 years ago.
- Gen's feelings for Amame are first alluded to here, where Komeji introduces her as the beautiful Amame Doi.
- Komeji is the announcer for the contest, even though he died six years ago. This is never commented on because Komeji is actually still alive at this point in time.
- Mizuki finds out in chapter 2 of her route that Jin Furue has the left half of Uru Somezuki's face, with his own distinctive percent-shaped birthmark on his right side. In Mizuki Chapter 4 M2, however, she appears to have no idea who the half-body found in Gen's freezer is, despite the fact that she should know exactly who it is by the birthmark. This only makes sense if the Mizukis are two different people, and the events happened at different times.
- In Mizuki Chapter 4, when told that Andes Komeji had been killed a few days prior to the date he was found, Mizuki and Aiba brush it off despite the fact that six years had supposedly passed since finding the two halves. That's because it really had been a few days, and a different Mizuki found half of Komeji after Ryuki did.
- More generally, the game starts with the discoveries of Jin Furue's two halves, with the left having been found six years after the right. When his left half is discovered to have an estimated time of death of only a few hours ago, the characters are understandably baffled by the clear contradiction. As more left halves are discovered afterwards and have also been found to have died six years after their right halves, the characters no longer comment on how little sense it makes - presumably, they are silently mulling over the impossibility of the information, but not voicing it as it is simply a continuation of an existing mystery. In the true timeline, Jin Furue was the only one whose times of death were out of sync - the characters didn't comment on the other ones because there was nothing strange to comment on. In other words, the game tricked the player into projecting their own confusion onto the characters.
- In Mizuki Chapter 4 M1, "Visions", Mizuki has the option to give Shoma a piece of chocolate since it's Valentines Day. Mizuki Chapter 4 M2, which is on a side path that can only be accessed after playing Chapter 4 M1 unless you already know the password in the Masked Woman's Somnium, also happens on Valentines Day, to which the option is again presented to give Shoma some chocolate. Doing so has Shoma question if Mizuki has offered him Valentines Day chocolate before, to which he then dismisses as déjà vu. Shoma isn't actually remembering some time that this Mizuki offered him chocolate, he's remembering the time "Bibi" offered it to him 6 years earlier.
- Also, in Mizuki Chapter 4 M1, both Date and Tokiko end up showing up despite how players are led to believe that they are both dead by that point. And yet, Mizuki doesn't even ask about how they are still alive (despite Mizuki asking Date about where he has been in the past six years in the Amame and Gen route). This is a major hint at the true timeline of the game.
- Mizuki Chapter 4 M1 also has Kizuna getting kidnapped, and yet, Kizuna is perfectly fine in Mizuki Chapter 4 M2. There doesn't appear to be a Point of Divergence for why that happened, and thus, this gives another hint at the true timeline of the game.
- In Ryuki Chapter 2, Shoma becomes depressed at the mention of his dad and asks not to talk about him, and says he's all alone. It reads like just an oddly melancholy extension of their established tense relationship, but this conversation is actually taking place six years after Komeji's been murdered.
- In Mizuki Chapter 2, Mizuki and Aiba question whether Gen's unusual behavior is because it isn't actually Gen but someone wearing a Gen mask, although they promptly confirm his identity afterward. Later in the game it's revealed that Date had been masquerading as Gen during the events that take place in the present, which was done in order to stay concealed from Tearer while he investigates, and also allows him to uncover a secret which becomes instrumental in solving the true nature of Jin Furue's death.
- The very first scene with Amame is when Ryuki goes to Sekiba High to talk with Iris. There, she mentions that she and Iris are graduating soon and can only wear their school uniforms for a little while longer, implying that they want to wear them as much as they can until then, even when they don't have to. Yet when Ryuki runs into her over the next several days, she is sometimes wearing casual clothes. All the times she is doing so are happening almost six years after she graduated.
- Gen seems a bit inconsistent regarding his opinion of Ota. Whether it's just a few months after Ota took over his family's diner or after he's had years of experience, Gen flip-flops over whether Ota is an amateur serving half-assed food or a serious rival that poses a threat to his business. In the true timeline, Gen consistently regards Ota as unworthy during the initial investigation and as a good cook six years later.
- Kizuna invites Lien to a party to watch online videos on Valentine's Day mere days after they first met and he made a very bad, even creepy, first impression. He was even disappointed that other people were invited and it wasn't a one-on-one date, making him come across even worse. This is actually happening after he and Kizuna have been together for six years.
- The Masked Woman sometimes seems indifferent towards Ryuki, but is very annoyed and aggressive towards him at other times. All the times she is angry with him take place after he shot her with a stun bullet, making her heart condition worse.
- When Mizuki goes to get a horribly drunk Ryuki from Brahman at the start of the game, she refers to the left half of Jin's corpse she just found as "the one we couldn't find years ago". Strange, considering that he was only one of several corpses whose left halves were never recovered. Chikara and Komeji's left halves were actually found only the very next morning after their right halves and Tokiko wasn't even dead yet, so Jin's left half really was the only one they'd never found.
- A few characters such as Mama and Gen make offhand comments to Ryuki on February 14 about a rocket launch causing a stir in Shinjuku, with no additional context. They are referring to the "rehearsal" rocket launch witnessed by Mizuki, the Masked Woman and Ryuki on the roof of Misetan, which took place the previous night and not six years in the future.
- When the Masked Woman shows up at Lemniscate on February 13, Ryuki seems surprised and acts as though he's never seen her before - strange, considering he'd met and spoke with her at the warehouse district only the previous day. Not only was the encounter at Lemniscate indeed the very first time Ryuki had seen the Masked Woman, this was the chronological first appearance of the Masked Woman persona, as Mizuki Kuranushi had only acquired the voice modulator used to disguise her voice from Moma the previous day.
- When in the underground cathedral following the discovery of Tokiko's right half, Tama mentions to Ryuki that she won't be able to make data backups due to being so far underground. While true, it's a little weird for her to say this, as the network was down at the time and she wouldn't have been able to make backups anyway. This is actually happening in the present, six years after the network's issues were fixed.
- When examining Tearer's Somnium, neither Mizuki nor Aiba remark on the fact that it is taking place within the living space underneath Horadori Institute that they had examined two nights previous. This was the first time Mizuki or Aiba had seen this place - not only would the Somnium's real-world inspiration not be discovered for another six years, it wouldn't even be the same Mizuki that does so.
- Two for one regarding Tokiko's figurine. After declaring that she can resurrect herself to Ryuki, Tokiko takes the figurine off her desk and smashes it to make a point that her own life is little more than a bargaining chip to her. Later that night, Ryuki finds Tokiko's right half on her desk with the broken figurine clearly visible on the floor. A later scene has Ryuki visit this office again and this figurine is intact. This scene is set six years before Tokiko smashed it.
- During Ryuki's investigation, Tama will give statistics about disappearances. Including the number for "this week". This happens twice and the number decreases between days.
- After discovering the left half of Komeji's corpse, Shoma runs away and Ryuki gives chase. Shoma eventually runs into one of the cars on the Ferris wheel at the Misetan amusement park. Ryuki patiently waits for the car to return as midnight passes. When the car comes back, Shoma is nowhere to be seen, baffling Ryuki - all while Tama only seems to care that it is now Valentine's Day. At midnight, the narrative's perspective sneakily shifts to six years later, so Shoma is obviously not on the Ferris wheel now - while never shown, it's presumed that Ryuki did in fact catch Shoma when the car made it back around. Thanks to his mental instability, Ryuki, like the audience, also believes that it's still six years in the past.
- The morning after finding the left half of Chikara, Ryuki asks Tama to virtually re-create the scene for him. Tama expresses concern over his mental state and apparently finds the request unusual despite Ryuki's understandable desire to gain more information regarding a new, significant development in an investigation he is headlining. During the re-creation, Tama makes a few jokes at Chikara's expense, which can come across as Too Soon. This is happening six years after Chikara's death, so Tama's concern and confusion make perfect sense and her jabs at Chikara seem less tasteless. This is also the first scene following the narrative's first hidden timeline jump, so on a meta level, it follows that this scene in particular feels a tiny bit "off" as a way to hint towards things not being quite as they seem.
Regarding the true identity of the Masked Woman and their connection to other characters:
- An extremely subtle one is given when speaking to Ryuki after his Somnium is completed. He's mostly sobered up, and claims that "instead of seeing three of you, now there are only two." It sounds like he's still coming off his bender, but it's him casually talking about how there is a Mizuki Date, and a Mizuki Kuranushi.
- During a conversation Mizuki has with Shoma, she mentions that she has someone younger than her who is the most important thing to her in the world, even though no such person has been introduced to the player. It turns out that the person that's really important to her is Mizuki, "our" Mizuki. And the Mizuki who said it is actually her older "sister", whom "our" Mizuki is a clone of. This also is a reveal that you are only playing as "our" Mizuki for half of the time, the other half is playing as the older Bibi.
- During both Ryuki and Mizuki's routes, Boss occasionally mentions that she has a daughter. On a seemingly unrelated note, the Masked Woman's color scheme is Red and Black, just like Boss. In the end, the Masked Woman is revealed to be Boss's (adoptive) daughter.
- During Mizuki's story arc, sometimes there's some sort of mark on her leg during scenes and sometimes there isn't. That "mark" is the scar from when Mizuki got shot by Saito in the previous game. And it is relevant because whenever the scar isn't on Mizuki's leg, you are controlling another Mizuki, her older "sister" (more accurately, the younger Mizuki is a clone of the older Mizuki, made to iron out the heart defect that older Mizuki had while retaining the super strength.
- In the Masked Woman's Somnium, someone she wants to protect is depicted by a blue, pink, and white bunny. Much like Mizuki's frequent associations with Adorabbit.
- In Mizuki Chapter Two, Aiba explains to Mizuki who Iris is, which is odd considering that Aiba knows Iris is one of Mizuki's closest friends, and wouldn't need an explanation. Until you consider how this Mizuki never actually met Iris.
- Somewhat similar to the above, reading Boss’ profile in the “present” section tells the player that she is Mizuki’s adoptive mother, which one would assume she did since Date was presumed dead when Mizuki was 13. However, Mizuki herself is shocked to hear that Boss has a daughter of her own, which is a weird thing for her to not be privy to until it turns out to be because Boss didn’t adopt our Mizuki, but she did adopt a Mizuki.
- Mizuki giving two different responses to what the water at the shrine is used for is also another hint towards there being two versions of Mizuki in this game.
- The running gag with Kagami is back from the first game, with Mizuki forgetting his name upon their second encounter. Though if you pay attention, it's clear that this Mizuki legitimately hasn't met him yet.
- At points, Mizuki tries (unsuccessfully) to get Boss to raise her salary so she can buy more stuff like clothes. This is a bit odd, as she is the lone heir to both of her deceased and well-off parents, and even inherited the position of president at Lemniscate and owner of Sunfish Pocket, among other ventures Renju controlled. She's clearly working for ABIS because she wants to, not because she needs any amount of money from it. This is yet another hint towards there being two different Mizuki's, as it is only Mizuki Kuranushi that does this. In addition, because Boss is her adoptive mother, this isn't too far off from her asking for a higher allowance; Boss mentions that "her daughter" has been doing just that at other points.
- The masks in Boss's office? They look very similar in aesthetic to the mask worn by the Masked Woman. This hints at the connection between Boss and the Masked Woman. Namely, that she's Boss's adoptive daughter, they live together, and she is confirmed at the game's end to have lifted her mask from Boss's personal closet.
- At one point, Boss jokingly accuses Mizuki of slacking off on the job due to being unable to find any leads on the HB case. Mizuki responds indignantly that it's not like she's "looking for a lost TV remote in my couch or something!" Bit of an oddly specific and contextual retort. It makes more sense once you learn at that point you're actually playing as Mizuki Kuranushi, Boss's adoptive daughter, and the two are privy to each other's home living habits.
Regarding the truth about Amame and their actions and connections with other characters:
- Komeji's initial claim to fame was his skill at quiz shows, even netting roles as a host in a few himself. Amame also has a talent for trivia. Parents tend to pass their talents onto their children after all.
- The scene where Shoma discovers Komeji's body offers plenty concerning the connection between Amame and the Endas.
- Shortly before discovering Komeji's body, Amame is standing next to Shoma instead of Iris and Kizuna. He's her little brother after all.
- Pay attention to Amame's expressions when Shoma approaches the bodybag. She already knows what's inside, and is clearly contemplating whether to stop Shoma from opening it.
- The girls each have different reactions to Komeji's corpse. Iris is merely disheartened and Kizuna is terrified. Amame? She's too traumatized to even speak. That's her father in the bodybag, after all.
- The taxi driver that drove Iris's group to Studio Dvaita lets slip that when they got there, Amame rushed out of the car while Kizuna was still trying to pay the driver. She knows exactly what Komeji is looking for, and is terrified that Tearer might already be after him.
- Loads of it in Amame's first Somnium. Of particular note are the heavy focus on Andes Komeji and the presence of multiple items belonging to Shoma, the wrench being replaced with a split body during the Spot the Difference game, and the very obtuse questions and situations being posed at the end.
- When Kizuna's gone missing, Ota mentions being unable to get a hold of Amame, and went to Sunfish Pocket to try and find her only for her to not turn up there. Even when Iris eventually turns up later on, Amame is still nowhere to be seen. She's not doing anything suspicious though, she's most likely just holed up at home grieving over her father's death.
Other bits of foreshadowing:
- In the character profiles, both Aiba and Tama are noted to only be female due to their settings. Initially a rather innocuous but odd detail. Near the end of the game, we are (sort of) introduced to a third Ai-ball named Marco, who was said to be male compared to Aiba and Tama, though Kotaro Uchikoshi confirmed in late July 2022 that they were non-binary
and was only referred to as male due to a localization decision. We don't actually hear or see them though since according to Bibi, they are extremely shy and introverted. - Out of the five characters that end up bisected, Chikara's halves are very specifically arranged in a standing position - the characters even take the time to go over how exactly this feat was accomplished. This strange detail gains a little more significance once all the information is revealed: Had everything gone the way Tearer had intended, only Jin and Chikara, the two he held responsible for his misery, would've been killed - Jin's halves arranged horizontally at Studio Dvaita and Misetan, and Chikara's placed vertically at Sekiba High and Yoyagi Park. Drawing lines to connect each half to the other has them intersect at the stadium, where Tearer intends to complete the Nirvana Initiative. When Komeji stole Jin's left half, Tearer both got revenge and put his original plan back on track by bisecting Komeji and placing his halves, again horizontally, at the same locations as Jin's. It's easy to interpret the body positions as an additional layer of symmetry that Tearer intended. Meanwhile, the other two victims, Tokiko and himself, were never part of his plan and their exact positioning held no special meaning.
- Possibly taking the cake for the most subtle of all is hidden in the answer to the mystery of how the culprit managed to place Jin Furue's left half in the center of the stadium without leaving any prints behind. The monowheel robot that Shoma made carried the body while riding along the line splitting the field in half, making the tire track nearly impossible to see with the naked eye, especially if you weren't looking for it. One can easily draw a parallel between this and the answer to many of the mysteries regarding Jin Furue's two halves: Jin and Uru also had a "line" perfectly bisecting their left and right halves, and splitting them along that line made it next to impossible to tell that the two halves recovered by ABIS so far weren't from the same person.
