Spoilers Off applies to all Fridge pages, so all spoilers are unmarked.
- The entire game is narrated both from Junpei's point of view and in third person. As it turn out, it's Past!Akane looking through Junpei's eyes.note This gives some of the bottom screen's exposition dialogue new context:
- The narrator gives odd descriptions of corpses such as comparing them to a macabre crab with pizza dough spilling out. Those descriptions are actually being made by past Akane; how else would a 12 year old describe a corpse with such limited vocabulary?
- The narration sometimes briefly breaks third person before the major Wham Line: when Lotus beats up Junpei for saying her sign is the woman symbol with devil horns, the narration says "Such violence...".
- The narrator gets cut off when in the Safe ending, Ace draws his gun and puts it to Lotus's head. Past Akane can't keep up with things happening extremely quickly.
- Also, certain conversations, such as Santa talking about Cradle and Soporil, and Seven's past as a cop, we don't see them telling Junpei, instead the story is told to the player directly. Because Akane already knows.note
- The very last puzzle has the player turn the DS upside-down, reflecting that for the first time, Junpei is solving the puzzle and sending the answer to Akane, which is the opposite of you've been doing up until that point.
- In the Shower room where you find Snake's supposed body, Santa talks about how the human body dies at 75 degrees Centigrade after examining the thermostat. He says a human body could only get that hot if it was in a sauna too long or.... in an incinerator... And then he gets all pissy, because Junpei dismissed that as random trivia and hardly even noticed that Santa's mood withered as he talked about that. As in, here is one of the people responsible for this whole game, doing what he's doing no matter how cruel it is for all of them, in order to maintain his sister in a Stable Time Loop, opening his heart and baring himself in a moment of weakness because of what does the facts about thermal effects on a human body represent to himself and his suffering... Aaaaaand his sister's crush doesn't even pay attention. Jerk.
- When Santa finds the perfect Panty Shot angle in room 6, why does he tell Junpei to go get Clover, when June is actually in the room with them? Turns out June is his sister, and the two of them orchestrated the whole game.
- The "Previews" from the main menu. Why give the option to rewatch what is essentially a game trailer? They show you which doors need to be taken in order to unlock the True Ending. Subverted with one showing a shot of Lotus at the computer with dark eyes, as it may be hinting the doors not to go through (4 and 8) or she'll get angry at a remark, so you can't get the Safe Ending.
- Take a closer look at the 'Memories of Escape' option. They're listed in this order: the room you begin at, the four sections that lead to the True Ending, the three sections for the Safe ending, and then the remaining rooms (which lead to the Sub ending, the only other one with credits).
- In the knife ending, Junpei finds Lotus stabbed in a corridor, to only be stabbed himself shortly after. Junpei is unable to recognize his killer due to being practically dead from blood loss, despite seeing him leave. It turns out that it might be a subtle hint about his killer, even if only slightly. Ace has prosopagnosia. Of course, that might just be thinking too much into it.
- In the Axe Ending, Ace tells Lotus that he wants to show her something. After Junpei asks to see it with Ace, he responds with "Once I've shown Lotus, I'll show you." Needless to say, it hints about Lotus' death in the Knife Ending.
- In Door 6, Ace estimates about four engines of this size would power the ship. Ace has been on the Gigantic before (and its owner,) and recognizes the surroundings, He would naturally know the design.
- In the Second-Class Cabin, on the subject of the Titanic, June believes Stead telepathically saw images of his own future, namely his experience on the Titanic. A less subtle hint about Akane's own state (though she saw it through Junpei's eyes.)
- Throughout the game, Akane continues to insist that they can find a way to end the game with everyone alive, which seems to serve to highlight her naive and optimistic nature. At the end of the True Ending, we find out that she knows how the game works, and that it's designed for everyone to escape alive.
- Just about anything June says or does is so deep in the Fridge it's got freezerburn. She knows she's watching herself through Junpei's eyes. Her childike naivete, her constant optimism, her references to the Titanic and Stead seeing the future.. this is all stuff she's saying for her child-self's benefit, reassuring her that the answer she's looking for really does exist and that she can survive; Akane is living proof.
- If you go through the True Ending, you find out that the "9" door that you need is actually a "q". There's one other door with a Q in it though - the Captain's quarters! You need to go through there to reach the True Ending and find out about the true nature of the Nonary Game from Clover.
- What do the correct door paths to the True and Safe ending have in common? They're the only two possible paths that let Junpei partner up with every other participant at least once. Select any wrong door, and you'll miss out on working with one or more persons.
- Door 9, well, the various doors numbered 9, are behind door 6, which is both the number 9 upside down and Santa's number.
- During the doll-presentation flashback in the True ending, Junpei says to Akane that now that they're graduating from elementary school, "after June we won't see each other anymore". Word of God says that after the Second Nonary Game in which he gave her the alias "June", he never sees Akane again. (This is a brilliant Woolseyism; her original Japanese alias was "Murasaki" and had nothing to do with months.)
- And then we have Virtue's Last Reward, the sequel. Junpei and Akane do meet again, many, many years later... but her psychic abilities and the life she's lived have changed her so much that she's nothing like the girl he once knew. After she became June, they were driven apart for good.
- In the 'Safe' ending, Junpei learns from Santa Ace's real identity, and that Ace told him this himself. Given Ace already killed two people to hide that fact, why would he tell Santa? Easy; he didn't. Santa is one of the masterminds behind the game and knows exactly who Ace is.
- The 1st Class Cabin gives us this little hint to Snake's name, Light, on examining a lamp:
Junpei: Well, at least we've got light.
Junpei: H-huh? What the hell, man? It's... It's just a light.
Snake: O-oh... Of... Of course...
- The "Submarine" ending hints on Junpei, Seven, Lotus etc's killer. Lotus' wrist is missing a bracelet, Seven and the rest aren't (though Ace's is unseen,) and the remaining door is a 9. The only other known bracelets are the 2, and the 9. Do some number-crunching, and you will realise 1+8+9=18 is the only number that fits.
- Some other endings hint at this, too. The disappearance of Lotus' bracelet is also remarked on in the "Knife" ending, and in the "Ax" ending, Ace wants to show Lotus something special while Junpei remained at the elevator to wait for Clover and the others.
- In the True Ending you find out that the last "9" door is actually a "q." This works better in the Japanese version because the Japanese word for 9 is "kyu" and is pronounced like the English letter. This can be considered written around in the English version, when you realize that Zero never verbally says the last door is a '9': just the typed rules given to everyone where the font makes '9' and 'q' look the same.
- The digital root of the doors you go in determines the number of the person who gets the gun in the two endings where the gun goes into play. Safe ending is 586. 5+8+6=19, 1+9=10, digital root= 1. In the Safe ending, Ace gets the gun. True ending is 471. 4+7+1= 12, 1+2= 3. In the True ending, Santa gets the gun (at first).
- The gun is hidden in such a way that someone must put the correct cards with faces of the various characters on them into the correctly numbered cases to get it. Ace has no means of getting the gun without someone else's help.
- Should you choose to go back to the hospital room while searching for Snake, Santa will tell Junpei that he shouldn't trust anyone in the game, not even the person he's closest to. Being one of the masterminds behind the game, he knows exactly who can be trusted and who can't—the latter group including said person Junpei is closest to.
- Through the various endings, Junpei frequently has a Heroic BSoD where he becomes a 'shell of his former self' and is 'no longer Junpei.' In most circumstances, this is the result of June's death. Watching the events from the past, Akane's horror at learning of her own death is entangling with Junpei's, making it hard to tell who Junpei is any longer. The only time that Junpei recovers from these shocks quickly is when he confirms that she had died in the past; a shock, but a paradox that the both of them can push aside their despair for to try and puzzle through it.
- Also, when in the Captain's Quarters there is a spot where you can have a major plot conversation with Clover, but if you didn't satisfy the conditions for the conversation Junpei will remark about a sharp pain in his chest. Missing this part of the conversation leads to the ax ending where Junpei is hit with an ax. I interpreted the blow striking him in the chest as it didn't instantly kill him.
- Actually, it's implied that she chopped off his hand to get his bracelet off. This is the reason why she offers her hand to Junpei, rather than just striking him down in the first place; she wanted to sever his hand cleanly. This also explains how Junpei is able to see Clover walk away with his bracelet when it's not supposed to fall of until after it detects his death.
- There are actually three doors with the number 9 (at least, originally, before Zero changed the last number 9 door to a q). Remember the title of the game? 999.
- The key to the final room in the "good ending" has the Neptune symbol. The astrological sign associated with Neptune is Pisces, and the symbol of Pisces is two symbiotic fish swimming in different directions. Seems like some subtle foreshadowing of the ultimate significance of the Junpei/Akane relationship.
- Santa mentions his success on the stock market which first makes him look like an intended victim for investing in the corrupt corporate empire, but Word of God reveals this was actually the source of Zero's funds and enabled by her visions of the future.
- June's fevers and Seven's headaches indicate you are on an incorrect path, causing young Akane to burn and discrepancies within Seven's false memories. The exception is Akane's fever after Clover is threatened by the 9th Man; even though she planned for him to do that (or at least judged it acceptable collateral damage), the terror sparked in everyone by that event made the bad endings much more likely than they'd previously been.
- Either that, or it's because Junpei (and two others) open door  to check the 9th Man's body (with Akane's sudden fever/collapse stopping them, leading to a proper player choice between  and ). Akane's fever flares up whenever you choose a door that leads away from the True Ending. Even though it's scripted, opening door  technically counts...
- Everyone remembers Akane as dead, even in the true ending when she never died. Why? She planted the thought in their heads. The morphogenetic field is used both to implant ideas in the heads of others as well as to receive ideas yourself, remember, and Akane is clearly very, very good at accessing the field, and is a stronger 'transmitter' than 'receiver.' She also knew, upon exiting the incinerator, that she needed to have died in order to survive, and so she overrides everyone's memories of the event with the event that never happened, that of her being burned alive, resulting in false memories for all involved. This might also explain why June doesn't seem to know much more than anyone else about what the true path is - when young!Akane changed the perception of the events in the field she changed her own perception of events as well, which left her hazy on the details of what decisions led to what end.
- Zero Time Dilemma offers another but no less Fridge-Brilliant explanation: When C-team got their hands on the antidote Carlos had a vision of Junpei's death in the pantry timeline. Shifters can see other timelines and espers can resonate with each other amplifying their abilities. That's why they saw it. Seven might not be esper himself but he was surrounded by espers playing the Nonary Game, that's why everyone involved remembers both timelines.
- The joint digital root in alphanumeric of "I am Zero" is ... Almost certainly unintentional, but still cool.
- Another hint about the connection between June and Santa: when everybody is showing their bracelets, only they have sleeves covering theirs, which might also indicate that they're immune to the bracelets' constraints (being 0 and 9).
- It should have been obvious from the start that the nine players aren't on an actual sinking ship: both times when Junpei checks the flooded stairways, the water is described as being completely still, like a mirror. The water shouldn't be still - the ship would be, at the very least, bobbing on the waves!
- Why did June pressure Junpei so much on details about his kidnapping? Because she never saw it happen, and she has to perform it herself. She's relaying all the information to her past self for later past use!
- Why does The zero bracelet read as ? If you choose to not believe that it's "o", then it's simple: It's a hint that Akane (who has designated herself as "6", is in fact Zero).
- And if it is an "o", then in any base higher than 24, the letter o represents 24. The digital root of 24 is 6, and adding 24 to any number affects the digital root the same way adding 6 would.
- Snake shows in the Safe Ending that he has the willpower of a god. This is not anything recent, though: in the flashback of the first Nonary Game, he tells the other kids (as a little kid himself) what he got his sister, Clover, for her ninth birthday. Nine four-leaf clovers. Finding even one four-leaf clover is rare enough that it's considered a sign of good luck. Snake went out into the fields and picked up nine for his sister's birthday present. And let us not forget, Snake is blind. He did all this without seeing. His willpower is over 9000!
- The digital root of each set of numbered doors you encounter adds up to 9.
- First set: 4 + 5 = 9
- Second set: 3 + 7 + 8 = 18, 1 + 8 = 9
- Third set: 1 + 2 + 6 = 9
- Final set: 9 + 9 = 18, 1 + 8 = 9
- This makes sense because the original design of the (first) game was for everyone to get through the doors. Split up into a group of five and a group of four for the first two doors and the number 9 doors, then three groups of three for the other two sets. Because of how digital roots work, there is always at least one combination of the nine people that can and will work. The only reason there were problems as early as the 3, 7, 8 doors this time was because the number 1 and 2 bracelets were incapacitated in various ways.
- The game's writing is very clever about what doors show up when. For example, why do doors  and  lead to the Sub End, probably the worst outcome? During the 3/7/8 split, Snake is missing, and Ace stays behind. + = 3, meaning that someone will always get left behind if Junpei chooses Door . The same is true of the 1/2/6 split, where this time only Snake is missing, meaning that choosing  causes complications. The Sub Ending basically occurs if Junpei messes up the even splitting up!
- According to the Enneagram, each type will resemble a specific respective other when under stress or when at its strongest. Snake is a 5, which "disintegrates" with 7; Santa is a 7, which integrates with 5. The player sees Snake losing his composure and Santa at the top of his game with a common catalyst.
- Akane's behavior throughout the game, teasing Junpei, but also acting oddly innocent and seemingly not always realizing when she's doing something to turn him on. All in all, you could say she's acting more like a 12-year-old with a crush than a mature 21-year-old, couldn't you? She knew that her younger self was watching her and didn't want to do anything that the younger Akane wouldn't do, so she basically acted like a 12-year-old all game long. And, yes, from what little we can see from flashbacks, Kanny did tease Jumpy quite a bit when they were younger, though her teasing was obviously a tad more innocent in nature. In fact, her entire behavior could also be useful as a shield in case Snake broke his rule and talked about the first Nonary Game and exposed her identity as June, never mind the fact that she should be dead, she could always claim to have suffered mentally and never emotionally matured as a result.
- Ace knocks himself out in the hospital room, forcing the remaining players to go through the #7 and #8 doors and skip the #3 door, in order to cover up the murder of "Snake", actually Nijisaki. But those two doors lead to the acquisition of the Jupiter Key and the Earth Key, respectively, the former of which allows for access to the central staircase and thus the option to use the latter and the Saturn Keycard, acquired earlier, to unlock two new paths...namely, the paths to the #1 and #6 doors, the latter of which leads to the chapel containing the #9 doors and the former of which contains Musashisadou and the Uranus Keycard, the only astrological key obtained before said doors but used after passing through them. Furthermore, at this time, the group's total digital root is 7—which means that if the only two doors that they had as options were #6 and #1, absolutely no one would have been forced to stay behind. Door #3 and Door #2 are in fact entirely irrelevant to getting to the end! Ace, of course, knows this, which is why he tries to railroad the group into avoiding the unnecessary doors, as this will allow his crime to go undiscovered—or so he thinks.
- More importantly, Zero knows this, and intentionally set up the numbers the way they were—Snake, the one who would be temporarily removed from the game, as #2, and Ace, the one who would want to kill him, as #1—allowing for the use of the #3 door to "kill" him using their bracelets plus Kubota's—to railroad the group into avoiding Door #3 at the 3-7-8 split and Door #2 at the 1-2-6 split, because all that Door #2 held was an "alternate exit" that wouldn't help save Akane in the past.
- It's mentioned very briefly that Clover and Snake look nothing alike, despite being siblings (Junpei even wonders if they're actually related). June and Santa look nothing alike, either.
- In the true ending, Clover makes a list of all the doors June has gone through to point out that Snake's idea that her 6 is really a 9 isn't feasible, and then it's pointed out that Santa has gone through every one of those doors with her and so if his 3 is really a 0, it works. No one points out that in the path that leads to said true ending, Lotus also goes through every one of those doors. While there are plenty of obvious in-game reasons why Santa makes more sense, not the least of which being that Santa took June hostage and therefore still had to know that the combination of Ace, June, Lotus, and himself would get through a #9 door—and further, that the original plan to leave only Seven behind would've required splitting himself and June up, but leaving June and Lotus together, there's the fact that Lotus and June are split up on other routes, and the many espers in this scene might already know that. Or, more pertinently, the fact that the choice of which two people Junpei asks to help him re-open the #5 door at the beginning of the game is supposed to be meaningless. If you picked either Santa and June or Ace and Lotus, it'd immediately be evident that Santa, not Lotus, is the one who is locked to June!
- There's also the simple fact that 3+6 is basically the same as 0+9. Adding 8 into the mix as a bracelet that's not what it seems requires even more loopholes.
- In the library, you can find a book called Mindswap, which is about people switching bodies. Now consider all the shit Sigma goes through in Virtue's Last Reward. Foreshadowing, anyone?
- Many plot points run on the fact that adding nine will not affect the digital root. Santa and June capitalised on this to prevent their real bracelet numbers, 9 and 0 respectively, from being found out. They did this by never splitting up from each other and choosing the numbers 3 and 6 for themselves. 3+6=9, thus they, as a pair, do not affect the digital root.
- Why does June make such a big scene both when everyone's looking at the destroyed body of the 9th Man and, what everyone thought, was Snake? At first you'd just pass it off as a kinda realistic reaction to being in such a tense situation while seeing such mangled dead bodies. But then you find out she wouldn't be feeling like she was in a tense situation, and she was the one who set up both of the deaths. It could have just been to make herself look the part of the innocent. Although...it's highly likely she did it to get Junpei to focus on her and stop looking at the bloody scenes. She knew her 12 year old self was watching through Junpei's eyes. She did it so her 12 year old self didn't have to see the horrific scenes for any longer than need-be.
- In the true ending the final 9 Door turns out to be the "Q" Door. The digital root of Q, as a hexadecimal number, is 8. How many people survived the Nonary Game? Since the 9th Man dies on every route, the number of survivors who pass through the Q Door is eight.
- The 9th Man's death makes a good deal of sense, when you realize that 9 is the one number that is utterly useless in Digital Root besides being another number needed to pass through a door.
- Why do REDs and DEADs display asterisks instead of proper bracelet numbers? Because, if they did show numbers, the actual value of Santa's, June's and Cap's bracelets would be exposed immediately.
- Early on, Santa refuses to go through Door 5 because he doesn't want to get his new shoes stained with the 9th Man's blood. It sounds like a really stupid reason, right? Right. He actually has a really good reason not to go into Door 5, but he can't tell anyone. If he didn't express his desire not to go there, the other players might have asked him to come along and verify his bracelet. If he did that, the RED would inform of an error on the digital root, revealing that someone's bracelet number isn't what its display shows. After some trial and error with all possible combinations, Snake (for example — he's the smart guy) would conclude that Santa's number is not 3.
- A particular conversation in the 2nd class cabin.
Junpei: Are you hiding something?
Akane: What would I hide...?
Junpei: Well, I dunno. Anything. I mean, you're hiding it. How would I know?
- Zero's offer was genuine - with Nijisaki (Bracelet No is 2), Musashidou (Bracelet is the letter O => 24, 2 + 4 = ) and Kubota (Bracelet No is 9), Ace could've escaped with his co-conspirators of the Nonary Project. Add the fact that Santa and June could leave the game, and the alternate way of opening the Q door, it's entirely possible that every player could get out.
- The fact that there's a mirror in the 3rd Class Cabin happens to be very important in hindsight, as is the reason why there's an important item taped to it. It's so that Past!Akane can see who she's reaching out to and realize it's Junpei.
- It seems weird at first glance that Junpei can't figure out what's going on through Akane's head when they're examining the bedroom, especially when Elevator Scene shows that he can be quite horny himself. But he's mindlinked with 12-year old Akane who's still a child, she's too innocent to figure out what her older self is thinking and that confusion is rubbing off on Junpei.
- Akane's Japanese codename is Murasaki. The first syllable, mu, sounds similar the Japanese word for "nothing". In other words, zero. "Mu" can also be read as "six", meaning that Akane's codename of Murasaki, as well as Cap's real surname of Musashidou both hint at their bracelets being a mix of 6 and 0.
- It's also the Japanese word for "purple". Akane's original name can mean "red", and her brother's means "blue", which together make purple. And, of course, both are the masterminds behind Zero, which may be foreshadowed in a puzzle that requires you to mix a red and blue liquid to make purple.
- Virtue's Last Reward introduces Schrödinger's Cat as a concept, and thinking about it, Akane in this game can be considered a Schrodinger's Cat (with the caveat that you can see inside the box before you open it). Due to the effects of time travel and quantum physics, Akane is both alive and dead at the same time. If you do the right things to save her, Akane comes out of the box (the incinerator) alive. If you screw up, Akane's past quantum-collapses into her dying in the past and she winks out of existence.
- The Japanese cover shows the title inside nine boxes◊, which looks like a sudoku grid.
- This exchange takes a whole new meaning if you consider what happened to Young!Akane originally:
June: Jumpy, you lit the candle.
Junpei: Yeah. You want me to light your heart on fire?
June: Jumpy... Don't quit your day job, okay?
- The Safe Ending finishes with the time limit being hit and Zero being announced as the loser, after telling Junpei that he took the wrong route. Going through the True Ending, we find out that Zero is Akane and that she is using Junpei as her "transmitter", using the morphogenetic fields to see what he's seeing and escape the game. As we also find out, the reason she does this is because she winds up trapped in the incinerator and needs Junpei's help to solve the last puzzle and survive. Because Junpei took the last route, he didn't make it to the last puzzle on time. Thus, he was not able to help Akane solve it. Thus, Akane either drowned or burned to death.
- Thankfully due to the nature of the Timey-Wimey Ball that future never happened and in fact it was a part of her plans.
- Actually, due to the nature of timelines explained in the sequel, all the endings are canon. Safe was a colossal failure to save Kanny, but the information that was gathered from it was needed to be transmitted to the Junpei of the True timeline. This actually means that she not only experiences her theoretical death in the incinerator (depending on the idea of that was an idea incepted into Seven, Clover and Snake), she experiences death through Junpei at least three times.
- Akane's fevers happen because you weren't doing it right and she was burning to death in the incinerator. Furthermore, she may have suffered it several times, depending on your interpretation. It's a wonder she kept so much of her sanity...
- Junpei's "misunderstanding" conversation with June at the elevator is hilarious... until you realize it's pretty unlikely that June's description of drowning would've been "heard from people who have experienced it", as she claims. Instead, in this context she's probably describing her own experience of drowning in an alternate timeline.
- It's not so far-fetched that she has met or read about someone who was narrowly saved from drowning. But considering she describes the fuzzy, free-floating feeling right after saying "I'll go to Heaven," there might be something to this.
- Chances that Akane actually drowned are pretty much zero. Considering her fevers mean that young Akane is being burned in the incinerator, and the present game actually takes place in Building Q, she would have never had the opportunity to drown - unless, of course, you count her feeling it from Junpei's experience in the Sub ending.
- In the sequel, whenever the main character dies, he describes the free-floating in a void feeling each time. So we can pretty much conclude that this was what Akane was describing. If that is the case, then she is describing a very general after death experience that she could have experienced many times.
- Two of the ways that Junpei can die involve drowning: the Sub ending where, after getting stabbed in the back and falling into the moon pool, and the IOS exclusive Syringe ending, where Clover (thinking Junpei killed Snake) injects him with Ace's Soporil and shoves him into D Deck's flooded staircase face down. This matters because Akane watches things through Junpei's eyes for most of the game, sharing his experiences.
- The scariest thing about the sub ending isn't that almost everyone died. It's the fact that Snake is still trapped in the coffin and has to starve to death or run out of air while not knowing where he is and being trapped in a small space.
- Totally what I thought too. The same thing probably happens to him in the knife and axe ending because no one took the note.
- Unless Clover takes an axe to the coffin when she hears someone in there.
- Even worse, if she chopped the coffin open and found out Snake was still alive, not only did she kill everyone for no reason, but the two of them can't even escape because the final exit door is actually a q.
- Just imagine what would happen if this DID happen. If she doesn't kill him before knowing who he is, she'll certainly, dare I say it, become even MORE of a maniac. I mean, she killed everyone out of revenge for him, and then killed him in what could kind of be considered an accident. Most likely, this would end in suicide. And if she doesn't kill him, and merely hacks the coffin open to see her very much alive brother, what then? I can't even imagine her reaction. And then Snake's reaction to finding out she killed everyone!!! Who knows how that one would end! Thankfully, it never happened.
- It did happen, though. We just never saw it. The sequel shows that every timeline is canon, and that, in at least one of those timelines, each of these things happened.
- In the axe ending Young Akane says thatClover is surrounded by light. Where is this light coming from? The fire from the incinerator that she's trapped in.
- It could also refer to the fact that Clover and Snake are siblings, and Snake's real name is Light. She could be "surrounded by Light" in that his supposed death is causing her reacting and behaving in this way, which leads her to become vengeful and insane.
- Or, given Junpei's sudden compliance with her suggestions, it may imply that Clover, as a "transmitter" having a nervous breakdown, is warping Junpei's worldview to make him incapable of resisting.
- Think about the cryptic line from the Safe Ending ("You haven't lost... I have lost."). Now think about who is probably saying it. Ouch, Aoi...
- In the axe ending, Ace and Lotus go off so that Ace can "show something" to Lotus shortly before Clover shows up and kills Junpei. Now, think about why Ace would want to have Lotus alone. He has his  Bracelet and the  Bracelet. Chances are extremely high that he wanted to get Lotus alone, and kill her to take her  Bracelet (like what is implied to have happened in the Knife Ending,) with which he can escape by himself, or so he would think until he hits the q door and dies.
- Prior to the True End, every time that an astrological key is needed to reach the point where the groups join up again after splitting up at numbered doors, said key is found on that side of the door. The Uranus Keycard, however, is found behind Door #1, prior to going through the #9 doors, but isn't used until after going through the small #9 door—and based on the Safe Ending, it seems like the path from the large #9 door to the incinerator is a fairly straight shot, so it can be assumed that the link between the two paths is the Neptune Door, which the small-door group has to unlock because that's where the Neptune Key is found (similar to how the group that goes through the #5 door has to unlock the Venus Gate in order to allow the two groups to merge again). What would happen to the group that went through the smaller #9 door if the group going through the large door had taken the Uranus Keycard?
- Worse, the Safe Ending ends with Junpei back in the chapel, implying that the "Door to Before" is accessible to the large-door group right away. This means that even if the Sun Door had already been unlocked, the small-door group would have no way of returning to take the alternate route off of the ship.
- More like Fridge Squick, but from what I can gather, 12-year-old Akane is tapping into Junpei's mind throughout the game and can see and hear everything Junpei sees, including his inner monologues. With that in mind, look at this exchange again:
Akane: Hey Jumpy, do you want to take a shower together?
Akane: *giggle* Just kidding.
Junpei: Too late to take it back... My brain's already working out the picture.
- Morphogenetic connections can only be formed between two people who love each other (familially, as between Clover and Snake, or romantically), the same person in different periods of time, or two people who are in a very similar situation (like Past!Akane and Junpei). So, who was so important to William Stead that the 'echoes' of their death on the Titanic rippled BACK to him before the event even happened? How much of his loved one's agony did he see? This one is explained further in the sequels, although not directly: Stead was a shifter. He's also a real person who actually died on the Titanic. He simply shifted back after getting killed and described it.