The game's start-up uses the "This Is a Work of Fiction" message, explaining all the characters and events are fictional, which is quite odd, since it never appeared in the previous games. It turns out to be quite literal.
During the demo's class trial, there isn't enough room for the entire cast of V3 in addition to Makoto Naegi and Hajime Hinata, so Monokuma has Rantaro Amami and K1-B0 sit out. Who would ever think that one of them would actually be the first victim and not participate in any of the class trials?
During the prologue, the chapter title appears as normal, with the text perfectly straight. After getting their clothes from the Monokubs and are subjected to a blinding light before being put back where they came from, the chapter title is suddenly lopsided and everyone remembers their talents and background. A huge clue into the final twist of the game...
In the prologue when the Monokubs are explaining the killing game, Kaede has the following thoughts that hint towards the biggest twist in the game:
Kaede: A lie... More like fiction... Like a story on TV... A scenario so removed from reality, we can hardly believe it's happening.
Early in the prologue, before the first use of the memory Flashback Light, Kaede says a line that rather OOC for the Kaede we see in Chapter 1, foreshadowing the Flashback Light changed her personality.
Kaede: It made me think how rotten the world is...
Comparing In-Game and Pre-game designs, It's easy to miss because she doesn't have much focus, but Tsumugi is the only character to have drastic changes to her physique (her lip is different, the shape of her face and eyes change, and her skin becomes less pale). It's a subtle first sign that she's different from the other students.
Over the course of the game, characters occasionally but consistently use the words "lie" and "fiction" synonymously, one example being Trial 3 where Korekiyo declares that the accusations of him being the culprit are "just fiction".
The first "motive" in the Killing School Semester is Monokuma attempting a Total Party Kill with copies of himself while also giving incentive for the first killer to commit a murder by offering them a chance to leave the killing game without a class trial. This in itself is foreshadowing that Monokuma has been doing the killing game for a long time as he's no longer using motives to psychologically encourage participants to kill and is in fact forcing them to do it or directly manipulating them into doing so. Of course, by the end, it turns out that he's Only in It for the Money and has been doing this for 53 seasons.
A massive amount regarding a single twist: the "mastermind" being Tsumugi Shirogane.
The first time she meets Kaede and Shuichi, she asks them for their favorite Doraemon episode, with her stating that her favorite is episode 53, the one with security cameras and target practice. Fast forward to the final chapter and you'll find out that it was way more than just a random question.
Again, when you meet her for the first time, she mentions that the statue she has been looking at looks suspicious. The second chapter is one of the places where you have to put the key items Monokuma and the Monokubs give you.
The very first words out of Monokuma's mouth are a Death Note reference. Tsumugi later references Kira, so it's likely not a coincidence.
Monokuma: I am the god of this new world!
During the first trial, Korekiyo brings up the point of the culprit being the mastermind. Tsumugi instantly shoots him down.
Tsumugi can be found around the sealed door and hanging out in classroom C (the one where the Flashback Lights are made) during Free Time events.
In Chapter 5, Tsumugi is the one most reluctant to go along with Kaito's plan to fight Monokuma.
Later in Chapter 5, Kokichi claims that he is the mastermind. Tsumugi instantly reacts with shock.
The Flashback Light the group gets in Chapter 5 contains information that directly contradicts later revelations concerning Kokichi. That's because Tsumugi faked it so to try and realign the killing game.
Chapter 1: The scene where Rantaro paints Kaede's nails while a jealous Tsumugi watches takes on a new light after Kaede is executed for Rantaro's murder, and it turns out that Tsumugi orchestrated the entire thing.
Why is it that Tsumugi's face is not shown in the Chapter 1 execution, compared to everyone else? Is she actually elated?
During the first trial, when Gonta tells everyone that he was watching a documentary about bugs to prepare for battle mentally, Tsumugi asks if he was trying to imagine himself as "a giant mantis with swords for hands". She was referencing the execution she had devised for him, which we see three chapters later.
Early in Chapter 2, Miu takes a jab at Tsumugi's plain appearance, pointing out that without her glasses, she wouldn't be noticeable at all. Tsumugi replies that her glasses are in fact the only thing hiding her terrifying true form. At the time, it's easy to brush that remark off as the ramblings of a hardcore otaku, but come the final Class Trial, her words are chillingly prophetic.
After the trial where Gonta died, Tsumugi was the one to see Kokichi's completed message. It's very likely that it was not a coincidence that Tsumugi just so happens to see that message after Gonta died.
On a meta level, her English voice actress played Sayaka from the first game. Both of these women ended up starting the killing game in a way.
Her talent being the Ultimate Cosplayer is one of the obvious hints that make one indecisive. It's a more obvious hint to her being the mastermind of this game because it's one of the most meta concepts addressed in Danganronpa: a character who is the most talented at playing as other fictional characters, to the extent where she even says "Tsumugi Shirogane" is just another identity trick of hers.
In Chapter 3, when everyone was discussing how Tenko was murdered in the darkness, Tsumugi mentions that glowing paint could've been used to see in the darkness and kill Tenko that way referencing the first case of the second game (and, in turn, foreshadowing that Tsumugi has literally played the second game, since that's all it was in this universe).
In Chapter 4, when she and Shuichi are exploring her research lab, she asks him if he would like to live in a fictional world. And then the plot twist of the sixth chapter happens.
During the Class Trials, her podium is #8, located right in front of Monokuma's throne, the same podium as the real Junko's seat in the first game and fellow Dragon Mikan in the second one.
She's always part of the team that opposes Shuichi's during the Scrum Debates, with the exception of the first chapter, in which she doesn't participate (and is ultimately revealed to have set Kaede up).
Of the five characters who remain when at the final class trial, she's the only one who's never accused of murder, nor given any sort of character focus or development.
It's subtle, but there are a few rule changes that hint that the mastermind isn't Junko again. For example, when there's a double murder in Chapter 3, Kokichi asks for a clarification of the rules regarding multiple blackened. In every other game so far, Monokuma always insists that mutiple blackened at the same time won't happen, but here he spontaneously decides that only the first one counts, even though it's irrelevant since there's actually only one blackened in the case.
Foreshadowing towards Kaede being the "culprit" of Chapter 1:
After Kaede worries that just catching the mastermind wouldn't be enough, she stuffs the things she's holding into her backpack. You'll note that she'd earlier picked up a shot put ball and never said she put it down...
After arranging the books, Kaede notes that she likes Rube Goldberg-esque devices. But what she'd supposedly just done (arrange books so it would be difficult for anyone to use the vent as an Air-Vent Passageway) had no relation to that. Turns out, she'd actually created a Rube Goldberg device that used the vent and the books as a path to roll a shot put ball down to drop on the head of anyone who interacted with the bookcase hiding the secret passage.
Kaede's internal monologue pops up less and less often across the case- because if you heard it, it would give away that she was planning a trap, and later that she thought she was the culprit.
Kaede repeatedly encourages Shuichi to find out the truth even if it seems too horrible- because she believes that the truth he'll find at the trial is that she, his confidant and Implied Love Interest, is the culprit.
Kaede notes that after the first Class Trial, they'll know who the mastermind is. 5 chapters later, and she is correct- when they finally solve Rantaro's murder properly, they're able to pinpoint the mastermind. Pity it happened after Kaede was executed...
The first part of the Class Trial has Korekiyo suggest that the Mastermind lured Rantaro to the library by telling him about the hidden door and murder him there, and took advantage of Kaede's trap for it. The sixth trial will prove that this line of reasoning was exactly what happened, even if he thought the trap was just the camera setup at the time.
Later in the class trial, Korekiyo suggests Kaede is lying out of love for Shuichi, and comments that he has personal experience with being willing to do anything for a loved one. Chapter 3 shows who his loved one is and exactly what he's willing to do for her.
At one point in Chapter 4, Himiko suggests that K1-B0 should self-destruct to open a hole in the wall, thus making himself useful. This remark loses the humor behind it when he does just that at the end of the game to let the survivors escape.
The Limited Edition box (which is also the "box art" of the English demo) featuring K1-B0 shows his true identity when it was revealed in Chapter 6 as not only as the Unwitting Pawn of being the cameraman working for Team Danganronpa, but also as the In-Universe "Protagonist".
The pre-release promotional materials (like official arts and merchandises) often paired Kaede with Rantaro. Before the game's release, many people speculated that they will be the new Makoto-Kyoko pair. In truth, they are the first characters to die in the game.
At the end of the Chapter 2 investigation, Kaito claims that he can't die before he's had his first drink or gone to space. His execution involves him going to space- and he dies peacefully at the end of it, his dream fulfilled.
During the Chapter 2 class trial, Kaito claims that he hid inside the girls' restroom to escape Gonta, who was dragging everyone to his entomology lab. There's a hidden passageway in the restroom, but since Shuichi and Gonta are both male, they wouldn't ever have the chance to find anything hidden inside.
The opening has a silhouette with purple glowing eyes for every character except Rantaro, who directly becomes a shadow. This is likely a hint that, unlike everyone else, he knew what situation he was in due to his survivor status. In addition, when the students gather in the gym, he seems to understand exactly what's going on, unlike everyone else.
At the beginning of the virtual world segment in Chapter 4, after Kokichi and Gonta's avatars appear, it takes oddly long before Gonta reacts to his surroundings and the avatars. Possibly an early indicator that Gonta mixed up the "consciousness" and "memory" cords in his headset. It's also hinted back in Chapter 1 that Gonta is left-handed, as he lifts the manhole cover with his left hand. This is significant, because Himiko used the trick to remembering which one is her right hand as "the one I hold my chopsticks in", which would be reversed for Gonta.
Chapter 1's title ("Me and My Class Trial", with the first "me" being written in Kaede's speech pattern and the second in Shuichi's) directly alludes to the fact that both Kaede and Shuichi are protagonists.
When Shuichi discovers his Ultimate Detective Lab for the first time in Chapter 4, he examines a bookshelf and finds "about 50" files that document murders and the tricks involved. If you actually look at the bookshelf, you can count exactly 52 files. All of the murder mysteries that occur in Danganronpa V3 will probably be included in the 53rd file if there ever is another killing game with another Ultimate Detective among the cast. Additionally, it's mentioned the earliest among the files include drawings instead of photographs, tying into the fact the earliest killing games were fiction.
Before everybody uses the flashback light in Chapter 4, Kokichi tells Kaito that he doesn't have the balls to use the flashback light, which immediately provokes him into activating it. Come the class trial, Kokichi plays Kaito like a fiddle by making fun of him and his values, which nearly gets everyone killed by voting for the wrong culprit.
An early Monokuma Theater sequence has Monokuma complain about how long the series has been going on. As it turns out, the season that the Danganronpa reality show is currently in is the 53rd installment of the Danganronpa series overall.
In the trial intermission for Chapter 2, Monokuma suggests to skip to the next chapter. Monosuke then states that they don't know who the culprit is, which is followed by Monotaro asking about the previous victim's killer. This could be considered foreshadowing as how nobody really knows the true culprit behind Rantaro's death and how Kaede received a Miscarriage of Justice.
In addition, when Kaito comments on the crossbow early in the Chapter, he accidentally mentions that his injury still aches, when Kokichi would have had two injuries, rather than Kaito's singular.
There are a couple of hints that Kokichi was Good All Along:
In Chapter 2, Kaito suggested that it would have been better if everybody were to watch their videos together in which that was what Kokichi tried to do earlier in this chapter.
He outright calls Maki a worse liar than him, and he proceeds to out her true talent. From a Metaphorically True statement, Maki is a worse liar than him as Maki's criminal past is far more dangerous than Kokichi's criminal past as Kokichi's organization does not kill and only commits non-violent crimes.
Often times in the past games, some of the more Token Evil Teammates tends to show swirly◊ eyes◊ during their breakdowns. During Kokichi's◊ "breakdown"◊, his eyes remained the same and they did not show those swirly eyes.
All of the achievements/trophies regarding completing each chapter use TV scheduling terms such as "Sweeps Week" and "Graveyard Slot".
When describing her backstory to Shuichi, Maki states her personality was broken down to be molded as the people training her to be an assassin saw fit, which is exactly what happened to the rest of the cast before the killing game began.
Junko Enoshima's arrival in both the first and second games, as well as within Ultimate Talent Development Plan, is in her queen persona. In V3 proper she uses her rocker one, a hint that it isn't really her.
The first five culprits have their Fatal Flaw overshadow them the most throughout the game, and display a great possibility of their identity as the chapter's main antagonist.
Kaede assumes that no one will kill anyone even when a time limit that guarantees everyone will die simultaneously is started. This foreshadows how paranoid she is as the assumption is in itself a logical fallacy.
Kirumi is a character who would adhere to any request. Therefore, the motive videos showing someone's special acquaintance would make her be the most submissive to Monokuma.
Korekiyo constantly talks about love in the story, his sister in Kaede's Free Time events, and directly tells the player that he has the appearance and personality of a potential culprit during the investigation of Rantaro's murder.
Gonta suffers from an extremely low self-esteem, which leads him to defer to everyone else's decisions instead of ever trying to think for himself due to belief that he is an idiot and other people know better than him. This leads him to giving Kokichi the benefit of doubt despite everyone else already knowing that Kokichi is up to no good and should not be trusted. Gonta also asks Kokichi's permission to converse with Shuichi after Chapter 1 out of fear that Kokichi would do something bad to him if he randomly disconnected from their bond, suggesting that Gonta believes Kokichi isn't above hurting him, which is proven true to a truly horrifying extent in Chapter 4.
Kaito's ideology of believing in others and not suspecting others would lead him to believe that working with someone else who wants to end the Killing Game (who turns out to be Kokichi, as Chapter 4 reveals) can create a plan that would actually end the game.
Very early in the Chapter 1 trial, Kokichi declares he knows who the culprit is. The Monokubs are shocked, since if he's right, he would set the world record for fastest class trial. They then reminisce wistfully about the previous record holder's amazing performance in trials and mourn for him as he is apparently dead. Initially, it just seems like the kubs are spouting random nonsense as usual, but with the revelation of Rantaro being the Ultimate Survivor who won the previous killing game, they were probably talking about him. Monokid's lament that he "soared through the enemy fleet all badass, just to die like a little punk" fits with this, since simply being snuck up on and bashed over the head would be a horribly anticlimactic and disappointing way for someone who was most likely the previous game's protagonist to be killed.
As mentioned under Artistic License – Music in the general example pages, "Der Flohwalzer" is played on mostly black keys, but is played on only white keys during Kaede's execution. Kaede is not the blackened.
The rule forbidding killing more than two people is conspicuously absent this time around. Probably because there's no need for such a rule as long as everyone follows the script.
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