There's a number of lines that become this to do with twists in the game: Right at the start of the game, Phi says to Sigma, "Back off Grandpa!". Sigma's reply indicates he's confused at the odd choice of insult considering him and Phi are only a few years apart at most. At another time, Dio refers to Sigma as a "senile old fart". When Sigma tells Phi his age, she retorts with "You must have done a lot of drugs". Alice seems that Sigma reminds her of her father. Then the twist comes that Sigma was actually an old man the entire game.
When Sigma says he's studying for a PhD, the others mention that he must have been studying for it for a while. Which can come off as odd, considering Sigma's only a young adult, and still at a normal college age. But of course, everyone thinks they're talking to an old man.
There's a number of times when the characters will tell Sigma he should rest, only for Sigma to refuse. Them suggesting for him to rest makes a lot more sense when you find out he's running around as an old man.
Sigma mentions several times throughout the game to the other participants that he was abducted in the early hours of Christmas morning, and admits to Alice and Dio he believes the date could still be late on the 25th. He's not technically wrong, as the game began on January 25, 2074 but he's completely off with the month and year.
His next comment, That it may not even be the 25th anymore could also be correct, due to the effects of Radical-6 on their perception of time. By this point of the Nonary Game, the date could well be January 26.
In Alice's ending, we learn both Ace from 999 and Dio are connected to Free the Soul. Despite the age difference, the two men seem to look remarkably similar. Could it be possible that Ace is also a Left clone, which at the very least contributed to his prosopagnosia?
In G-OLM's explanation, the girl in the Chinese room bears a deliberate resemblance to Luna. Not surprising, as Sigma visits the GAULEM Bay in the Luna END timeline.
Why is everyone freaked out by Sigma being a pervert and making passes? It's understandable to find it gross, childish and off putting from a young man, but typically it's not considered creepy, which is what a lot of the reactions seem to indicate. Obviously they'd find it creepy. From their perspective, a old guy with a robotic eye keeps making dirty and sleazy comments.
Why does Sigma have such a hard time noticing details sometimes? Often they'll play off on a joke where he'll not notice something, and the others in the room with him will berate him for being a blind idiot. One example is when he fails to notice that the completely not-normal looking clock with no hands wasn't a normal clock. He's only got one real eye.
If the entire point of kidnapping Sigma and Phi was to be able to go back in time and stop the outbreak of Radical-6, then why was Sigma kidnapped a week before the outbreak even happened? How would they know that he was the right person, and it was the right time to kidnap him? Well, since Akane is an esper connected to Junpei, she was able to see into the future through him, and know about the Radical-6 outbreak. Perhaps Sigma became a great scientist in that future, who showed hints of being a time-travelling esper himself. Of course, at that point there was nothing he could do about it, as his skills weren't sufficiently developed. Thus Akane preemptively kidnaps Sigma days before the incident, then examining the possible futures (as she did in 999) creates the circumstances necessary to give them a chance to stop the plague.
Dio thinks he's breaking into the game to disrupt it. Little does he know that the game intends for him to enter. Why? Because, if you remember 999, the Nonary Game only works when there's real danger involved, and he's the Ace of this scenario.
For a circus ringleader, Dio seems to know a surprising amount about genetics; he even helps Sigma solve the themed puzzle in the Laborarory. However, this makes sense when Dio's true identity as a clone of Left is revealed.
In addition, the Nonary game needed a common enemy amongst the players, and since Dio was the one who planted the bombs he snugly fit the bill. This would then form a sense of trust in the rest of the players, making them choose 'Ally' until everyone could escape.
Dio seems to find the pictures of Saturn's rings in the astronomy magazine especially interesting. Hardly surprising, since they're made of debris from Saturn's destroyed moons.
Why did Tenmyouji tell Alice that her body is made of Ice-9? Consider the fact that Clover went around and told everybody that Alice is the same frozen mummy from the urban legend as a joke. This suggests that "All-Ice" became an in-joke among the characters involved since they picked up Alice in the middle of the desert and learned about the urban legend before they escaped. Tenmyouji was basically trying to tell Alice who he really is because he was one of those people that knew the joke.
It could also be interpreted as a playful jab at the players (read: the real-life players!) who were confused by seeing Alice at the end of 999.
Or he really did believe it. Junpei did wonder a lot at the possibility back in 999.
Consider Sigma's inner monologue for explaining why he's in the Nonary Game
"Had I started a fight with a frightening and mysterious new religion? No... Had I hacked into some terrorist group's server? No... Had I witnessed an assassination? No... Had I gotten wasted and had a one night stand with the mistress of a prominent politician? Well, yes... But it was just the one time..."
How many people think most of these things are all feasible things that Sigma could do in the upcoming third game? Perhaps some brilliant foreshadowing there.
When you think about it, the ones he hadn't done as of yet when he has that monologue are all things he ends up doing throughout the game!
Consider the things mentioned here, and then remember what's special about Sigma. It's probably not a coincidence that he thought of these specific examples.
The Sequel Hook: Consider the implication that Sigma and Phi's first attempt at preventing the release of the virus fails, then think about the final node in the flowchart that is supposed to be from Kyle's point of view, but hints that it's the player in Kyle's body. Sigma and Phi won't succeed in their mission until the player attempts it with them!
On a meta level: Why can't Phi tell "Kyle" about what happened on the Mars mission? Because spoilers, obviously!
And how does Akane know what you are? Being the player character, technically, of 999 probably helps.
The illustrations in the past (Akane and the explosion) are in 2D, as opposed to the 3D from the rest of the game. It seems like a device to show that something's changed, until you realize Sigma only has one eye, so he doesn't have any depth perception.
On the other hand, Sigma's kidnapping was also illustrated in 2D, and that was prior to his losing an eye.
That was in third person, however. The examples given above were in first person
The doors on the maps have three kinds of markings to show what they are: colors for Chromatic Doors, gray for doors that can't be opened, and blank for doors that can be unlocked. The big door in the floor B Warehouse is blank.
Everybody's impressed with Sigma's photographic memory. Having a robotic eye probably helps with that.
Also, no one expects an old man to have such a good memory.
K enjoyed the kiddie ride so much because his own childhood was deprived of playful experiences.
During the talk with Alice in the B. Garden, she makes an off-hand remark to Sigma: "You remind me a lot of my father". This might seem a sweet, albiet strange thing to say to someone who's younger than her. To Alice, Sigma is most likely around the same age her father was/would have been if not for his murder.
In several routes, after the first AB Game, Sigma remarks that he is still working on his doctorate, which Alice responds that he "must have been working on that for quite a while".
At one point in the game, Sigma tells Phi his age. Phi remarks that Sigma must have done a lot of drugs to look way older than he does.
In one of the timelines, Dio calls Sigma an "senile" which is an odd statement to say to someone who's supposed to be 22 years old.
All those times where Clover was creeped out by Sigma's sexually suggestive replies and actions? Justified considering his real age.
Sigma remains clueless about his body's age until the very end where he finally finds a reflective surface, because the only other exposed skin he can see in his outfit are his cybernetic arms, which were probably deliberately made to look youthful. This also justifies how he is able to pin Dio to the ground or grab a hold of his leg in other timelines, his body is 67 years old but his cybernetic arms are youthfully strong
Because of the game's 3D art style, some of the characters end up on the wrong end of the Uncanny Valley. Luna by far is the hardest to look in the eye. After the Robotic Reveal, however, I immediately understood why K rejected her. I don't know if that was intentional (especially since everyone else is much easier on the eyes in their own ways), but if it was, that's one hell of an Intended Audience Reaction, not least of which is due to K eventually coming under the control of the player.
You can pick up a secret file containing "Knox's Ten Commandments" for writing detective fiction, written by the author Ronald Knox. The game gleefully breaks every single rule, and here's how:
1) The criminal must be mentioned early on. Akane and Dr. Sigma Klim are not mentioned by name until the final routes.
2) All supernatural or preternatural agencies are ruled out. Completely destroyed, as psychic abilities are a cornerstone of the plot.
3) No more than one secret room or passage. There are several in the game.
4) No hitherto undiscovered poisons may be used, nor any appliance which will need a long scientific explanation. The use of fictional chemicals and technologies such as Radical-6, Soporil Betanote which admittedly was talked about some and used on the players in the previous game, the CAS treatment podsnote CAS was briefly mentioned by Ace in the previous game, Ice-9note Which was importantly mentioned during the route to the True Ending in the previous game, Tubocurarine and Neostigmine note Which are two real chemicals, but require some technical knowledge to understand and recognize before the in game explanation. In general, the game is dripping with technobabble.
5) No-one with extra-sensory perception or similar powers can appear. See number 2.
6) No accident must ever help the detective, nor must he ever have an unaccountable intuition which proves to be right. Several times, most notably to unlock the "Where did Alice go?" story lock.
7) The detective must not commit the crime. The player character discovers that he, as in his older self, is Zero Sr..
8) The detective must declare any clues he may discover. This rule basically means that the detective can't solve mysteries using clues that he hasn't discovered and declared; in other words, no whipping out a sudden Deus ex Machina clue for a twist ending. Thanks to his timeline-jumps giving him the answers, Sigma solves a lot of mysteries he has no clues for, like when he exposes Dio's true identity..
9) The stupid friend of the detective- the Watson- must conceal nothing from the reader. Phi is more intelligent and aware than Sigma is, and actively hides secrets from him. In addition, up until the end of the game, the game conceals a major fact from the reader(which all the other characters are aware of) - it takes pains not to show Sigma's face.
10) Twin brothers, and doubles generally must not appear unannounced. The reveal of K's true face.
The other reason this game gets away with breaking every single rule is that it follows the "spirit" of the rules while spitting in the face of the letter of the rules. A "Fair-Play Whodunnit" basically is supposed to present you with all the possible information you need to form a conclusion ahead of time. Virtue's Last Reward certainly does that. The restriction against psychic powers and twins and such is so that writers don't perform an Ass Pull, but here, Magic A Is Magic A.
The original version of Rule 5 is "No Chinamen (read: Dirty Foreigner) must appear in the story" (because it'd be too easy to single them out as the bad guy). Guess what, the game breaks this rule too! Dio is Obviously Evil and a terrorist (the modern era's bogeyman). In fact, he's so obviously evil that it wraps around to being completely surprising when it turns out he's the bad guy. Luna also breaks this rule: if the the essence of the rule is "Don't put in a character who is a red herring suspect just because they're foreign", then Luna breaks it since her route is that she is suspicious because she is a robot.
Also, Zero III is dressed as Chinese Opera сharacter.
Number 8 is lampshaded by Sigma. He justifies it by mentioning that the clues are still the same regardless of the branching paths.
Most people would place Phi's recurring quotation of "I am no man" as a Lord of the RingsShout-Out, but the phrase was also said by Odysseus to the cyclops Polyphemus. With that in mind, Phi likely said it to take a crack at Sigma's missing eye.
The moment the shit really hits the fan for humanity is on April 13th 2029. That's right, the 13th day of the fourth month. Which is also a Friday. For added kicks, the digital root of 2029 is 4.
And for an additional OMG moment, the detonation of all of the reactors occurs one day before the 115th anniversary of the sinking of the Titanic, the moment that forever changed Dashell Gordain's life and led him to create the first precursors to the modern Nonary Games. The day that Sigma leaves for the Moon with Clover, Phi & Alice in tow takes place on the day of the anniversary proper.
How did Tenmyouji know who Zero was in his ending? Run through it after watching the Phi ending. He watched Dr. Klim's recording when he went to re-acquire his picture of Akane, which only makes sense when you find out that Klim and Sigma are the same person
In the same way, why Zero Sr orders to Sigma to NOT talk about what he saw in the recording ? Imagine if he tells to the others what Zero Sr looks like...
The reason Zero III appears as a rabbit is a reference to the "Moon Rabbit" in East Asian folklore.
Why Zero is a rabbit, part two: Okay, so it's a reference to the rabbit on the moon. In the Chinese version of the story, a mortal woman named Chang'E accidentally drank a potion that caused her to float to the moon and become immortal where she meets the rabbit living there. Akane is the closest thing to being immortal in this series.
Part 3: Zero III was created by Dr. Klim, but designed by Akane. Remember Akane's traumatic childhood experience involving rabbits?
During Luna's route, Phi wonders aloud if the Nonary Game could be a Chinese Room experiment. In a way, she's right. The information is relayed from others in the alternate timelines, such as K and Luna (the Chinese people) and relayed to their immediate situation (ex: the computer login screen) without Sigma actually understanding what it all means (at least until he catches on during Phi's route).
A small but somewhat clever one. In round one of the AB Game, the Sun Card is used only once, and in the second AB Game, the Moon Card is again only used once, and for the third AB Game and beyond the Star Card can be used as many times as the players need too. Why the Star Card? Simple. There is only one Sun and Moon visible from the Earth's point of view or so the players think..., and there are countless of stars, reflecing the unlimited amount of uses the Star Card can have compared to the Sun and Moon Cards.
Luna may not be totally Three-Laws Compliant, but on the other hand, it's probably not a coincidence that she always picks "Ally".
Another bit of brilliance regarding the Chromatic Doors: The only routes where you make it through the white Chromatic Doors are the ones where the colors of the previous two doors you went through mix to create white.
Luna Route: Magenta(Red+Blue) + Green = White
Tenmyouji Route: Yellow(Red+Green) + Blue = White
Phi Route: Cyan(Green+Blue) + Red = White
Dio's outfit and back story refer to his position of leading a terrorist group, the Myrmidons, a subdivision of Free the Soul. As their ringmaster.
Speaking of Dio: while his behavior does him no favors by ensuring everyone chooses to betray him, it's a perfect cover for his actual mission. He presents himself as a sociopath who never thinks about anything but himself; what better cover for the leader of a terrorist group known for a bizarre lack of individuality and selfhood?
Every escape room over the course of the game is clearly labeled with what kind of a room it is. The final one is simply labeled "Q". Thus, a door that leads to your escape is a door that carries a "q", just like it was in the first game. Tenmyouji's reaction, as a Nonary Game veteran makes sense too.
The final route has enough locks and gates on it that, either directly or indirectly (that is, the route that does contain the key to a lock had locks of its own) requires you to see the ending of all nine routes. While getting to that room required passing through a bunch of other locks, the final one doesn't appear until you're about to exit said room. The key to logging onto the computer in the Q room was found at the end of Quark's route.
So, what's wrong with the sink in the infirmary, causing the slow drain that Sigma remarks on when you turn the faucet? Not a darn thing. The sink's working as intended, but Lunar gravity isn't pulling the water down the drain as quickly as Earth gravity would. Sink's fine. Gravity is broken.
This is one of the few things Radical-6 can't compensate for (similarly to Phi's jumping abilities), since you can measure how fast the water is going down by the height the liquid reaches, which won't be affected by your perception of time.
What does K's name stand for? Kyle. Or, if you save Akane, then it's Kanny. Or Kurashiki
Luna says that the reason she didn't stop any of the murders on the path to her ending was because she was afraid of death - or, well, whatever death means for her; being deactivated, or what have you. That's heartbreaking enough on its own, but remember: that path takes you (and Luna) through the GAULEM Bay. She saw GOL-M explode for saying too much; it's understandable she'd be extra wary of stepping out of line! And considering that she did just that by hacking Zero III and reviving herself, that only speaks further volumes about the kind of bravery that must have taken, and depths of the bond she had forged with Sigma by that point. Also consider the possibility that maybe she (and not Zero III) was the one that really deactivated GOL-M, fearing that he was about to reveal her true identity; in her ending, she seems to want so desperately to be accepted by Sigma for what she is. After the reveal of Sigma's true identity, this may seem a bit weird; she would, of course, know that Sigma is really the one who created her. But the younger Sigma's consciousness inhabiting his older self's body wouldn't have known that! However you choose to interpret the events of the GAULEM Bay, it makes Luna such a beautifully tragic character.
It could possibly go deeper: Luna is very much 3 laws compliant, albeit she was likely tweaked with the Zeroth law (substitute "human" for "humanity") to account for her inaction as humans come to harm (since it's for the sake of humanity). However, the third law stays very much in effect. A robot has to protect their own existence as long as such protection doesn't clash with the first two laws. Seeing GOL-M explode might have actually prevented her from going any further as she could have been placing her own life in danger (or alternatively, she would have been in danger if GOL-M unmasked her, since there's no way anyone would buy that a robot was uninvolved in the grand scheme of things). However it seems that Luna actually goes out of her way to subvert the third law (and likely the second) because of her love for Sigma.
Why does the Mysterious Woman talk so slowly in the audio? Probably so that the others can understand her words while under the effects of Radical-6.
The English title has two meanings, as the main page explains. But it also has a third- the titular virtue is diligence, which a player must have to get the true ending; it requires playing through everyone else's paths, and paying attention to the story's finer points. The ending is literally 'virtue's last reward'.
Whenever someone calls Zero III a rodent of some sort, he insists "I'm a rabbit." Whenever he's referred to as such at a point where he's not actually present (e.g. Phi calling him "Algernon"), Sigma's quick to point out that he's a rabbit. Foreshadowing that Sigma was the one who programmed Zero III?
Pay attention to the nicknames Zero III gives everyone. The ones he gives to those affiliated with him are not actually that insulting, while everyone else's are.
Sigma and Phi only really start to get their act together in the third branch of the story (Cyan Door), where they start to realize what's happening to them and are better able to keep their memories as they jump. Why the sudden improvement in their abilities? Is the repetition of jumping finally having an effect? Or is it the fact that in the Cyan timeline, there's an additional esper in the party to boost their power?
On the same train of thought, if Sigma goes through the Yellow door with Tenmyouji, he begins to cotton on to the fact that he's living the same events multiple times a lot faster than he does if he goes through the Magenta door with Luna. Tenmyouji, a.k.a. Junpei, is also a psychic, and Sigma is likely absorbing his powers a lot more directly in the Yellow door route.
The above also establishes Sigma and Phi as incredibly powerful espers, as it is said that stronger espers absorb the power of weaker ones nearby - and Akane, who before this was the strongest named esper, does not seem to be limiting Sigma or Phi's abilities, meaning that they are leeching off of HER. While it's never stated by anyone outright, this might well be the reason that they were chosen for the AB Project, as Akane could tell that they were stronger than her.
Why does Phi always advise Sigma to pick "betray" after the first round of the Nonary Game? Picking betray always leads to the best possible outcome for Sigma. If he betrays Luna in round 1, he progresses to the Dio ending where he gets to escape alongside Dio and Phi. If he betrays Tenmyouji in round 1, he progresses to the Clover ending where he learns information critical to getting K's ending. Neither of these endings require you to have played any other paths in order to win. Finally, betraying Alice in round 1 puts him on the path to Phi's ending, which is the game's Golden Ending and ends with everybody surviving.
Complete the game, then play the entire thing through on "skip". That's exactly how the events would be taking place if you took away the effects of being on the Moon.
In one of the secret gold files, it's revealed that the GAULEM you meet in the GAULEM BAY's product IDnote GTM-CM-G-OLM stands for GAULEM Type Male - Cockney Model no. G-OLM. Taking from this, we can fill some gaps in Luna's product IDnote GTF-DM-L-016 and get GAULEM Type Female - Diana Model no. L-016, with the L most likely representing "Luna."
In the Lounge you get an article that talks about the lunar eclipse in December 28, 2028. It does match the date in real life but a player who did some research will know that it can only be seen in the Eastern Hemisphere. Sigma is from California and the game has implied that you have been abducted to Nevada. In Dio's ending, you get to see the lunar eclipse, which should clue you in that something's wrong.
If you play the Pantry room on Easy Mode and fail too many times on the ice cube puzzle, you get insulted by Clover saying that her awesome brother could solve it. For those who forgotten or never played the previous game, he's blind. It was a Stealth Insult.
It's pretty clear that Sigma can remember each time that he is killed. That's chilling in of itself, but when you consider that this ability is shared by other espers who have become "unstuck", it's clear that Akane most likely remembers being burned alive. No wonder she was never quite the same after escaping the First Nonary Game.
This one came as one to me. Sigma and Phi both have the ability to swap places with their other selves. However, what happens to the consciousness of the one in the past when say one of the bombs explode in the future. According to in-game they swap, so in the end you send your past self into a future where he dies anyways. At least that's how this troper took it.
Take this a step further... In this game, Akane say Junpei sent his consciousness to the past to save her from the incinerator. With how we know this works now, what does that change about 999's plot? For one, Akane was looking through Junpei's eyes does that mean her consciousness was present in Junpei for the bulk of the game? In this game's final ending, we have an unnamed consciousness in K's body and he thinks that he is K. In that sense was the Junpei we were playing even really Junpei at all? If the consciousnesses are supposed to switch to make room what else does this say about the final puzzle of 999 when Junpei sends his consciousness back in time to solve the puzzle?
That's not quite how it works with their powers. The Morphogenetic field is essentially an information relay and the branching possibilities of the events occurring - Akane and Junpei's powers as Espers are linked only into those specific uses. Junpei doesn't send his consciousness back in time - he sends the steps to the solution of the incinerator puzzle to young!Akane in the past and that's it. Phi and Sigma on the other hand, can broadcast their consciousness -through- time itself, displacing their future or past selves in a body swap, and Akane's gambit with the Nonary game is to cultivate this power to its maximum in order to set right the Mars Mission Test site disaster, where Free The Soul boobytrapped the base and placed the virus. This time-traveling power is necessary, and Akane herself states that even with her power it is impossible to stop the outbreak of Radical-6 without help from the timejumpers Phi and Sigma.
It is very likely that Quark was trapped for all eternity in the treatment pod and would probably never wake up again in Clover's Ending, as everyone had killed themselves due to the Radical-6 virus taking over their minds.
In none of the timelines was Quark put into cold sleep, so he would probably get up once the anesthetic wore off. And then he would stumble upon the bodies... if he even made it that far.
The treatment pods are said to have locks on them in the K Ending. However, none are ever used until Dio is put in one. Quark would be able to leave. Finding the bodies or succumbing to Radical-6, however, are still possibilities.
Luna would still be able to move around. Because everyone else is dead, she'd have no reason to act like she's dead, and she could help Quark.
Then there's the bad ending where Tenmyouji carries Quark through the number nine door, despite his own bracelet not having nine points. I'm sure Quark will be thrilled to wake up alone next to his dead grandpa.
Clover tells Sigma that she's strengthened her psychic bond with her brother to the point that they can communicate telepathically at will, but she's been sending out messages to him nonstop since arriving in the warehouse and hasn't heard back yet. She wonders whether there's a stronger esper nearby interfering with her signal, as it were, and it turns out she's right, but even if she hadn't been...since she was kidnapped, the world has experienced a viral pandemic, a nuclear winter, and a 45-year time elapse. He's almost certainly dead. Even if he did happen to survive, he's spent the last several decades in a Crapsack World and probably has no idea what happened to his sister. Given the reasons for Clover's abduction, it's also possible that he was taken around the same time for a different project (the next game, maybe?) before the pandemic, but you know something's wrong when that's the best-case scenario.
Why the "Lion eating the Sun" motif? Because all of this comes from Akane and her desire to get revenge on Cradle because of what Ace/Hongou did to her. In 999, Junpei describes him as looking like a lion, and Akane wants revenge because he locked her in an incinerator.
Anytime someone reaches 9 BP and escapes through the 9 Door. Whoever escapes usually thinks they'll be able to get help on the outside, but they don't realize there's nothing out there for them on the moon. Whoever else survived would potentially be trapped inside the warehouse for life... which wouldn't be long, due to the Radical-6 infection inevitably leading to their suicide.
Dr. Klim spent several decades at Rhizome Nine with three Human Popsicle cases for company. He only built Luna when Kyle asked and was very surprised at the request, and Akane joined him after that! Given that we never get a chance to talk to him directly, his personality in the third game may be... not very sociable, and certainly different from the way Sigma is.
Considering this gives new meaning to his studies. Cloning, Artificial Intelligence, and Robotics, all of which he could use to create new people. (In most cases) He knew ahead of time that he would need to make Kyle, Luna, Zero III, G-OLM and all the other Gaulems, but it's also likely that he threw himself into his studies so that his creations could relieve his loneliness. And remember that Sigma was a 22-23 year old College student when he made it to the moon. It probably took him a long time to build anything significant.
It was stated in the Q & A that Akane orchestrated Sigma's breakup with his girlfriend and it's possible neither of them knew the truth. Alas, poor unnamed character.
Actually...as we discover in Zero Time Dilemma where we do indeed interact with the 67 year old Dr. Klim in Sigma's body, he originally wasn't all alone when he first started living on the moon, as Diana joined to help him. But then Diana died about three years later from a circulatory illness from the moon's weak gravity, and this event was what truly prompted Sigma into creating Luna, both out of necessity for the AB Games and out of loneliness after her death. Granted, while he's better adjusted than expected, it's still clear he spent most of his time on the moon alone after Diana died.
A retroactive Fridge Horror for the previous game: in 999, some of the horror of the game's bad endings was mitigated somewhat by the idea that Akane was merely watching the possible branching paths to study and learn puzzle answers from, and not fully experiencing them. This gave the impression that none of the endings where Junpei died really happened, as it was merely Akane seeing what was a POSSIBILITY to happen, and not a true account of what was absolutely going to happen. Come this game, and we learn that all of those timelines actually occur. While it's true that Akane only sees them from afar (unlike Sigma and Phi, who experience them firsthand), they still have to actually happen for her to witness the results. Meaning that Junpei and the others really did die in several timelines.
We learn in Luna's ending that ABT, or artificial biological tissue, is held together by muscle fibers. When turbocurarine is applied, it causes the skin to tear/crack. In Alice's bad ending, Sigma, who has only 1 BP, is betrayed by Alice, who was thought to have unconscious at the time. The skin of his cybernetic arms is made of ABT, so that means once he dies, not only would the cast believe Alice killed Sigma, but they also have to see Sigma's arms gruesomely fall apart.
On December 31, 2028 Radical-6 gets released from the Mars Mission Test Site. On April 13, in response, humanity blows up 18 antimatter plants. It took only four months for the complete collapse of humanity, and for the survivors to decide to kill thousands of people directly, and then millions more through a nuclear winter.
With a certain reveal in Zero Time Dilemma a retroactive nightmare appears. In K's ending, Sigma is forced into a situation where he must give the neostigmine to either K or Phi, since he only has enough for one. With the reveal that Phi is actually the daughter of an alternate Sigma, the situation turns from "which of my friends do I save before I die?" to "which of my children do I sacrifice so the other can live?". It doesn't alleviate the situation even with the knowledge that neither Sigma, Kyle, or even Dr. Klim knew of this fact.