Warning! All spoilers below are unmarked.
Island mode is canon.Island mode is not a "what if" scenario, but the solution the survivors found to bring everyone back, resetting everything to before the mess started and not allowing Monokuma to steal the administrator position, allowing everyone lives solution.
Izuru was the mastermind behind The Biggest, Most Despair-Inducing Incident In All Of Human HistoryIn the final trial it seems that Enoshima is terrified of Izuru/Hajime when he emerges, which puts to doubt the relationship between them, it's possible he actually was the mastermind behind everything that happened in the backstory, using Enoshima as a figure head after she "corrupted" him.
Dangan Ronpa shares the same universe as Fallout.The SHSL Despair happened in the year 2077, but was planned decades in advanced by Junko and Mukoro's parents, who were also with SHSL Despair. The nuclear weapons that started and ended the Great War were launched under the influence of SHSL Despair. Furthermore, Hope's Peak Academy, before the Despair incident, was with Vault Tec Corporation, and Jin Kirigiri was working with them. When the students of the first game locked themselves in the academy, they were actually using trying to develop it into a Vault, which went south when their memories were taken by Enoshima. It's also a possibility that Future Foundation is a division of Vault Tec. Remember Tranquility Lane from Fallout 3? Well that could easily use the same technology as the New World Program.
Super High School Level Despair is the Product of a Hope's Peak ExperimentJunko is described as being born with a hunger for despair. Considering how much influence and technology the Hope's Peak Board of Regents have, she could have been a failed Kamukura prototype. Considering to her data analyst abilities in Dangan Ronpa Zero she probably was made to acheive the ability to analyze everything and use them for the cause of hope, but due to a messed up 1/0 binary imput on the idea of hope... The other SHSL despairs could be seen as experimentals as well, and the Despair Fever victims are simply reawakening their memories of botched experiments to create Kamukura's way of thinking.
Gundam suffers from Chuunibyou (eighth-grader syndrome).If anyone is familiar with Chuunibyou Demo Koi ga Shitai!, then it's pretty obvious that Gundam is having the same kind of delusions that several of the characters in that series do; he hasn't recovered from them and still fancies himself a dark overlord.
Gundam is the one who cut out his own eye so that he could see despair.It was mentioned specifically in game, and it would explain why one of his eyes is gray and scarred, when the other one is red. Who else has gray eyes? Junko Enoshima.
Souda, as part of SHSL Despair, was the one who built the contraptions for Junko's executions from the first game.Even though Junko may be the Mastermind and designed all of the executions to fit her friends' despair, I doubt she's smart or talented enough to to build some of them herself, such as the rocket ship from "The Space Journey". But, there someone who is and who would do anything for her: SHSL Mechanic Souda who can build and fix anything.
The Despair Disease is actually Radical 6 from Virtue's Last RewardBoth are Spike/Chunsoft and both are diseases whose main symptom is crushing despair
The Junko body SHSL Despair found was a fake.Take a look at the execution from the previous game, the girl is nigh invulnerable.
Fauxgami is actually Togami's brother.Togami's final FTE in the first game states that he and his relatives played a game to determine who would be the heir of the family. Everyone who lost to him was disowned and treated as though they did not exist, a status that would be befitting of a SHSL Imposter who has no true self. A more in-depth reasoning can be found here.
Peko was never corrupted by Junko's despairShe just went along with it because Kuzuryuu did.
Nidai is actually SHSL Eyebrows.Ishimaru was super jealous.
Owari was the student who starved herself for despairThere are two students who love food, one of these is Owari. At the end, we see a picture of an emaciated, leathery hunger worn student. Who would go deeper than Owari into despair without food? It's been speculated that Monobear wanted to mock the students for what they did: for example, the above speculated Kuzuryuu plucking his eye out, and in Chapter 5 Monobear starves everybody until a murder is committed, and Owari is still alive in that chapter.
Nanami is still aliveWhile she probably didn't survive the Forced Shutdown, the copy of her on Jabberwock Island was probably not the only copy of her. As an AI she can be copied onto alternative hardware. Seeing as Alter Ego had multiple copies of himself, Nanami probably had a few back-ups as well. Still, any copies of this nature wouldn't have firsthand memories of Jabberwock island outside of what Monokuma broadcast. Note that this means that AI Junko probably has copies as well, but since Izuru Kamukura would probably be their proprietor, it wouldn't be too much of a chore for him to destroy them.
Usami is inspired by Alter Ego's late-night talk with YamadaAfter all, he was the most enthusiastic about magical girls, and Alter Ego was eager to learn about his interests. He's also one of the only students besides Fujisaki that Alter Ego's known to have an extended conversation with.
The person Mikan was talking about at the end of Chapter 3 was Izuru Kamakura.Specifically, the person who she "loved" and ended up killing for. It could have been Enoshima she was referring to, but Kamakura is another possibility. After all, it would explain the times during Chapter 3 where Mikan ended up falling asleep on top of Hinata. Perhaps, having regained her memories, she recognized him as Kamakura.
Gundam's final spell was not intended to protect himself.When he collapses on the ground, he doesn't look surprised or upset that it didn't protect him. This suggests two possibilities:
Cybernetic brain implants were involved in the surgery that turned Hinata into Kamakura... and the computer involved had just enough storage space for copies of Nanami and Monomi's programs to hide themselves until their respective Big Damn Heroes moments at the end of Chapter Six.
Dangan Ronpa 3's theme will be a Cultural FestivalThe first game's theme was "killing school life". This game's theme is "killing school trip". The next game should be about a "killing school festival".
For Dangan Ronpa 3, there will be other forms of Zero Escape shoutoutsFor example, the protagonist will be SHSL/Ultimate Memory and the game will play with branching paths like Virtue's Last Reward. The only way to get to the true final level would be to go through every path, then fight the Mastermind (Most likely Junko) with everything you remember from each branch.
The fact that the game takes place inside a computer simulation and the player character Hajime Hinata is Big Bad Izuru Kamakura is meant as a Take That towards the player themselves.As Monokuma would probably put it, you don't care about the students, they're just characters in a video game! And you want them to suffer despair and die! If you didn't, then why did you play this game? The first Dangan Ronpa ended on a bittersweet but ultimately hopeful note, and you could easily have simply accepted that as the ending and left the series alone! It was YOU who chose to play the sequel and see more despair! YOU are the one who wanted this!
Dangan Ronpa 3 will take place at least six years after the second game.Based off what we know from Another Episode, It's possible that the Warriors of Hope who survived that game will show up as high-school aged students in the third game. Perhaps, in that amount of time, the world has recovered enough from the Despairing Incident that the Future Foundation will attempt to open a new Hope's Peak Academy.
Izuru kamukura's plan was (supposedly) to destroy SHSL Despair.We know from Absolute Despair Girls that Komaeda has a literal love/hate relationship with Enoshima, loving her and hating her at the same time. It is possible that Izuru shares the sentiment: they're both deeply connected to hope (Komaeda deeply believes in Hope; Izuru was supposed to be the Ultimate Hope) and despair (Komaeda has his constant cycle of good/bad luck; Izuru started the Incident). So, while they follow Junko, they really hate her and everything about her.
The Five who were mentioned in the final debate.They are the five survivors as only five were mentioned. It was one last jab at the five survivors to give them reasons why they should graduate. If it were Mikan who tried to have children with Junko's corpse or Gundam who cut out his eye it wouldn't have quite the same impact.
Nanami may have not been the one who killed KomaedaSure, Komaeda is SHSL Luck so he might have got the traitor to throw it. Even if that isn't true, who could have said otherwise? Monokuma has seen who had thrown the actual poison. However, he also wanted the Future Foundation spies to be dead but isn't allowed to touch them. Therefore, he could have used the opportunity to use the voting to kill Nanami, regardless of whether or not she killed Komaeda. This would act as a mirror to trial 5 of the last game where Monokuma did try to pin the blame on Kirigiri since she knew too much. However, since there is not SHSL Detective, he could get away with it this time.
Nidai is wearing a protective cupThe shape of his bulge looks too even to be you-know-what, so it's likely he's wearing one since his field of expertise probably requires it. Furthermore, when he turns into Mecha Nidai, he no longer seems to have the bulge. That would make sense, since a robot wouldn't need any kind of protection down there anyway.