* [[spoiler: 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.]]
* [[spoiler: 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.]]
** [[spoiler: 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.]]
* [[spoiler: 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.]]
** [[spoiler: 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.]]
* 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..."
** [[spoiler: 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 [[spoiler: things he ends up doing throughout the game!]]
*** Consider the things mentioned here, and then remember what's special about Sigma. [[spoiler: It's probably not a coincidence that he thought of these specific examples.]]
* The SequelHook: [[spoiler: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: [[spoiler:Why can't Phi tell "Kyle" about what happened on the Mars mission? Because spoilers, obviously!]]
** And how does [[spoiler:Akane know what you are? Being the player character, technically, of 999 probably helps.]]
* [[spoiler: 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 [[spoiler: 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 [[spoiler:his losing an eye.]]
* 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. [[spoiler: The big door in the floor B Warehouse is blank.]]
* Everybody's impressed with Sigma's photographic memory. [[spoiler: Having a robotic eye probably helps with that.]]
** Also, [[spoiler: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: [[spoiler:"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. [[spoiler: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. [[spoiler: Phi remarks that Sigma must have done a lot of drugs to look way older than he does.]]
** [[spoiler: 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? [[spoiler: Justified considering his real age.]]
* [[spoiler: 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]]
* [[spoiler:Because of the game's 3D art style, some of the characters end up on the wrong end of the UncannyValley. Luna by far is the hardest to look in the eye. After the RoboticReveal, 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 IntendedAudienceReaction, 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. [[spoiler:The game gleefully breaks every single rule, and here's how]]:
** [[spoiler:''1) The criminal must be mentioned early on.'' Akane and Dr. Sigma Klim are not mentioned by name until the final routes]].
** [[spoiler:''2) All supernatural or preternatural agencies are ruled out.'' Completely destroyed, as psychic abilities are a cornerstone of the plot]].
** [[spoiler:''3) No more than one secret room or passage.'' There are several in the game]].
** [[spoiler:''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 Beta[[note]]which admittedly was talked about some and used on the players in the previous game[[/note]], the CAS treatment pods[[note]]CAS was briefly mentioned by Ace in the previous game[[/note]], Ice-9[[note]]Which was importantly mentioned during the route to the True Ending in the previous game[[/note]], Tubocurarine and Neostigmine [[note]]Which are two real chemicals, but require some technical knowledge to understand and recognize before the in game explanation[[/note]]. In general, the game is ''dripping'' with technobabble]].
** [[spoiler:''5) No-one with extra-sensory perception or similar powers can appear.'' See number 2]].
** [[spoiler:''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]].
** [[spoiler:''7) The detective must not commit the crime''. The player character discovers that he, as in his older self, is Zero Sr.]].
** [[spoiler:''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 DeusExMachina 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.]].
** [[spoiler:''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]].
** [[spoiler:''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 "FairPlayWhodunnit" 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 AssPull, but here, MagicAIsMagicA.
** The original version of Rule 5 is "No Chinamen (read: DirtyForeigner) 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! [[spoiler: Dio is ObviouslyEvil 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.]]
** Number 8 is lampshaded by Sigma. [[spoiler: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 ''Film/LordOfTheRings'' ShoutOut, but the phrase was also said by [[Literature/TheOdyssey Odysseus]] to the cyclops Polyphemus. With that in mind, [[spoiler: Phi likely said it to take a crack at Sigma's missing eye.]]
* [[spoiler: 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, [[spoiler: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]].
* [[spoiler: 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]]
* 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: [[spoiler: 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: [[spoiler: 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. [[spoiler: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 [[spoiler: 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 [[spoiler:ThreeLawsCompliant]], but on the other hand, it's probably not a coincidence that she [[spoiler:always picks "Ally"]].
* Another bit of brilliance regarding the Chromatic Doors: [[spoiler: 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.]]
** [[spoiler: Luna Route: Magenta(Red+Blue) + Green = White]]
** [[spoiler: Tenmyouji Route: Yellow(Red+Green) + Blue = White]]
** [[spoiler: Phi Route: Cyan(Green+Blue) + Red = White]]
* Dio's outfit and back story refer to [[spoiler: 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, [[spoiler: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 [[spoiler:simply labeled "Q"]]. Thus, a door that leads to your escape is [[spoiler:a door that carries a "q", just like it was in the first game.]] Tenmyouji's reaction, as a [[spoiler: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. [[spoiler:The key to logging onto the computer in the Q room was found at the end of '''Q'''uark'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? [[spoiler: 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.]]
** [[spoiler: Radical-6 should compensate for that, though.]]
* What does K's name stand for? [[spoiler: Kyle. Or, if you save Akane, then it's Kanny. Or Kurashiki]]
* Luna says [[spoiler: 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: [[spoiler: 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.]]
* Here's [[http://images2.wikia.nocookie.net/__cb20121228225442/ninehourspersonsdoors/images/7/74/TenmyoujiOfficialArt.PNG a piece of Tenmyouji official art]]. [[spoiler: [[http://fc07.deviantart.net/fs71/f/2010/358/5/c/junpei_999_render_by_willowtruise-d35ks5g.png Now look at Junpei]].]]
* Why does the Mysterious Woman talk so slowly in the audio? [[spoiler: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'.
* [[spoiler: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. [[spoiler: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? [[spoiler: 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. [[spoiler: 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 [[spoiler:Quark]] was trapped for all eternity in the treatment pod and would probably never wake up again in [[spoiler:Clover's Ending, as everyone had killed themselves due to the Radical-6 virus taking over their minds.]]
** [[spoiler: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.]]
*** [[spoiler: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.]]
** 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 [[spoiler: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...[[spoiler: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 CrapsackWorld 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? [[spoiler: 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. [[spoiler: 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 HumanPopsicle cases for company. [[spoiler: 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, [[spoiler: and certainly different from the way Sigma is]].
** Considering this gives new meaning to his studies. [[spoiler: 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.]]
* 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 [[spoiler: 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 [[spoiler: 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 [[spoiler: 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.]]
* Major spoilers for Tenmyouji: [[spoiler: I did have a difficult time to accept that his full name is Junpei Tenmyouji. Tenmyouji sounds a bit unusual for a Japanese surname that you would think Clover and Alice would have pressed him about it. Hell, there could have been a scenario where they would ask him about a guy named "Junpei" and he could have easily lied by telling them he's his grandson.]]