Junpei, a normal 21-year-old college student, arrives at home one night to find his window open. Upon closing it, he spots a cloaked figure in a gas mask in the reflection—and the last thing he can remember before passing out is being told that he's just been chosen to participate in the "Nonary Game"...He then wakes up in a third-class room on an early 20th-century ship. Upon escaping from there, he finds out that he's trapped on the ship with eight other people who were similarly chosen, and forced to play the game lest the bombs planted inside their bodies go off. Needless to say, things get worse, and they're forced to trust each other and race against the 9-hour time limit to figure out what's happening and why they're on the ship.The first game in the Zero Escape series, 9 Hours, 9 Persons, 9 Doorsnote in the original Japanese: Kyokugen Dasshutsu Ku Jikan Ku Nin Kyū no Tobira?, lit. "Extreme Escape: 9 Hours, 9 Persons, 9 Doors, or 999 as it is sometimes known, itself plays as one part "escape from the room" games, one part Saw and one part story (though some self-labelled story segments offer the player numerous choice points). Decisions made during story and escape segments determine how events unfold and which characters will interact. There are several branching paths and your decisions impact the ending.It sadly never was released outside Japan and North America. Even then, most game stores had to specifically request the game to stock. As an original DS game, it can be imported and played on any DS and 3DS.A sequel titled Virtue's Last Reward (in the original Japanese, Kyokugen Dasshutsu ADV Zennin Shib˘ Desu, or roughly, Extreme Escape Adventure: Good People Die) was announced for the Nintendo 3DS and Playstation Vita in August 2011. It was released in Japan on February 16, 2012, and released in North America on October 24 2012. It was released in EU territories and Australia the following month.In February 2014, it was announced that due to low sales in Japan, production for the trilogy's last game was being put on hiatus. Fans have started a Facebook campaign to show support for the series.Despite the use of spoiler tags, this page contains many spoilers by virtue of not being entirely whited out. Somewhat surprisingly, 999 is still possible to play completely unspoiled and most walkthroughs are spoiler-free as well.
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Abandoned Hospital: A large part of the ship is a converted hospital. Some of the rooms are pretty creepy.
All The Worlds Are A Stage: The game's final escape room has remixed versions of previous puzzles. The last puzzle of the room recreates the teams formed to pass through the numbered doors. Including a "9" door. The solution requires you to leave one box empty, while the other box has five numbers (players). Those present, in the puzzle, are the five you exit the incinerator with at the very end of the game. Those missing are Akane, Aoi, Ace, and The Ninth Man.
Area 51: Building Q, out in the middle of the Nevada desert, where part of the Nonary Project experimentation is carried out ... and also where the events of the game, unbeknown to most of the cast, play out. In a nod to the real status of the site, it is a private building of a multinational rather than a government building.
Not necessarily true - said Event Flag comes from picking up the red key, which Junpei would have to have anyway, in order to get the briefcase open. All you really need from the room are the two keys, which are in very simple locations, and it's entirely possible to bypass every other part of the puzzle.
Arc Number: You have to ask? Nine. To be specific:
The Nonary Game itself: 9 victims, 9 hours to escape, numbered doors from 1 to 9, 9 seconds before the numbered doors close when they open them, and 81 seconds (nine squared, and 81 has a digital root of 9) to find the detonator-deactivation-scanner once inside
Speaking of ages, the digital root of everyone's age? Ace (50) + Snake (24) + Santa (24) + Clover (18) + Junpei (21) + June (21) + Seven (45) + Lotus (40) = 243 = 2 + 4 + 3 = 9. The 9th Man doesn't count, unless his age is a digital root of 9 on its own.
In several parts of the game you use different bases substituting a letter for an extra number. Taking the whole alphabet into account (A=10, B=11...Z=35, 10=36), if you substitute the letters in zero for numbers you get 35+14+27+24=100.
If you got the True Ending, you'll have gone through nine puzzle rooms. Furthermore, the final puzzle in the True Ending is a sudoku puzzle, which is all about sets of nine.
Various bits of dialogue from examining things in puzzles can result in conversations like:
Ace: "There's nothing in the drawer anymore." Junpei: "Nuh-uh, there's air." Ace: "How old are you, 9?!"
In the Captain's Quarters after telling Clover about the bookmark Santa gave you she takes 6 paces to the left, 6 paces to the right, then 6 paces to the left. 6+6+6=18 > 1+8=9
A key aspect of the game revolved around the calculation of digital roots. Although not explicitly stated, calculating a digital root is mathematically equivalent to calculating the number modulo 9note Unless the number is a multiple of 9, in which case the modulo is zero.
The solution to the safe puzzle is 14383421. Multiply this by 9 and you get 129450789, the true number of each character's bracelet.
It may be unintentional, but the digital root of the numbers of the bracelets the four Cradle Pharmaceutical members wore during the game is 9. 1(Hongou)+2(Nijisaki)+6(Musashidou's true no.)+9(Kubota) = 18, 1+8 = 9.
All Is Well That Ends Well: Junpei more or less feels this way after the Game ends, if his pursuit of June is any indication. The reactions of everyone else subvert the trope.
Artificial Limbs: Snake. His left arm is conveniently able to be manipulated so that he can slip his bracelet off, though he keeps that one secret. It's also a major plot point, proving that the corpse believed to be Snake, against all odds, is not actually Snake, because it has a broken bone in the left arm.
Asshole Victims: The planners of the first Nonary Game. Arguably, the nine players themselves are stereotyped so that any one of them may be this, and it's not until character development kicks in during New Game+ rounds that the trope is defied.
It possibly occurs after every puzzle except for vital items such as keys. However, the keys are removed from your inventory but still shown to be in your possession so it is possible that you still have everything else.
If you beat a puzzle without using all the items and look at the items again before you fully leave the area Junpei will say something about him not knowing why he's carrying the item and he will throw it away later. Which only makes sense, why would you run around carrying a ripped shower curtain all day?
Also Seven has been shown to use some of the items to hold the doors open so the group can backtrack.
Junpei pulls these off in a few scenes in order to force the teams to divide in a way that lets him through his choice of door.
Ace does the same thing, too, in the hospital room, forcing the teams to divide in a way that wouldn't allow anyone through Door #3.
In the Safe Ending, Junpei exposes Ace by pretending that he switched clothes with Santa. Ace's inability to recognize faces caused him to fall for the trap and reveal himself as the game's villain.
It's eventually revealed that part of the purpose of the Nonary Game is to punish the four Cradle executives who ran the first Nonary Game. This is partially accomplished by tricking Ace, the CEO, into killing the other three. Though Ace is never forced to do anything, Zero knows him well enough to predict his actions.
Exploited brilliantly in the True Ending. The Second Nonary Game could have fallen apart in countless ways, as the bad endings illustrate. But Akane can SEE those bad endings and use the knowledge gained from them to steer Junpei through.
At the beginning of the game the Number Nine Man enters a numbered door by himself and explodes because of small bombs placed in his stomach, foreshadowing the rules for the nonary game. You have to walk past a bloody puddle of his remains if you chose to go through that door. Later on another man dies in a similar way when being thrown into the number 3 door by himself.
This game infamously has a number of bloody deaths for bad endings. Especially during the axe ending where Clover becomes literally Axe Crazy and brutally murders several people.
June is quirky, to put it mildly. After listening to her talk about automatic writing and possession, Junpei develops a headache. She seems to consider being trapped in a freezer the perfect time to talk about imaginary substances and chemistry. Justified, as the crazy superstitious talks are hints to the fact that she's a walking supernatural phenomenon.
Cluster F-Bomb: Except Snake and June. Santa is the primary offender, though.
Color-Coded for Your Convenience: A really clever bit of both Foreshadowing and Fridge Brilliance here; Clover and Snake both wear red and blue respectively. Why is this important? Clover was able to transmit signals, and Snake was able to receive them in the first Nonary Game. This is the same exact color used for the figures during the examples when the theory pops up in-game
This doesn't end there; June/Akane wears red in the first Nonary game, and she's meant to be a transmitter to Santa, a receiver. Santa himself has traces of blue in his design in the first Nonary Game. And finally, Junpei has both red and blue in his design, hinting at his ability to both transmit AND receive. June/Akane herself also wears purple, which is also the meaning of her name — a mixture of red and blue, which could also indicate her eventual ability to transmit and receive. True, while some characters like Nona don't wear red or blue despite being a transmitter, apply this to the main characters and it certainly fits.
Santa: Look, Ace! It's some kind of snowman secret meeting! Ace: Those are just bags full of sand. You use them as a counterweight when you're lifting something with a pully system. Santa: Man, you're too serious...
Companion Cube: In Room 8, have Junpei examine the mannequin more than several times for him to eventually dub it "Science Boy". His attachment to Science Boy can lead to a Funny Moment or two, especially after the fire breaks out. During the fire, try examining Science Boy and the door Clover went through.
Compressed Adaptation: When the game was ported to iOS, a lot of the puzzles were cut. Unfortunately, most of the game's characterization (and humour) unfolds in the various conversations had while characters solve the puzzle.
Computer Equals Monitor: Discussed. Lotus mentions this trope in conjunction with a wireless monitor and mentions how someone who wouldn't know better might just assume the computer is the monitor. This ties into the ongoing theme with morphogenetic fields and the theory of seemingly unconnected things passing information between them. It also adds to the Red Herring of Alice, who would presumably fall for the trope.
Contemplate Our Navels: Some conversations are guilty of this, but not nearly to the extent that the trailers would suggest. The game lampshades it hilariously in the True Ending: when Ace is about to start going to full-philosophical about his motivations for the Nonary Game, Junpei immediately has him gagged again.
Cooldown Hug: Junpei embraces June to calm her after she saw a dead body in the shower room.
Cool Old Guy: Ace. Except in the endings. In the Safe and True Endings, he's revealed to be the Big Bad. In the Submarine and Knife ends, he's implied to kill some, if not all, of the game's players.
Word of Godhas confirmed Ace is indeed the killer in the Sub and Knife endings.
Santa. You can always count on him to make some biting comment insulting Junpei's intelligence.
Also Junpei, in some instances.
Disabled Snarker: Snake goes throughout the game making sarcastic comments. He also happens to be blind, and if you make the mistake of underestimating him, he'll bathe you in snark.
Decoy Protagonist: An odd example: you learn at the very end that the protagonist is actually the June of 9 years ago, seeing things through Junpei's eyes. This is why you can start a new game with your memories intact, because even though Junpei dies, the 9 years ago June can start over. However, it could be argued that they are both the protagonist.
Description Porn: The visual novel sections tend to describe the grisly bodies in horrific detail while showing only an image of the general area around the body, not the body itself.
Development Hell: The third installment in the series is dangerously close to this, because the creators are unable to get funding for it.
Determinator: Snake in the Safe Ending. Seven, who pursued the original case nine years ago; Santa, who set up the second Nonary Game to save his sister; Lotus, who has spent nine years obsessively researching the cover-up; and Junpei also count.
Ace, throughout the game. And before. And after. And for all the wrong reasons.
Diegetic Interface: There is a reason this game has New Game+ - you as the player are playing from June's POV from the past as she witnesses all the possible futures Junpei could go through in his Nonary Game. Emphasized when during the True End, the player has to turn the DS upside down, as to now actually play from Junpei's POV while helping June.
Wordof God states that the game began with the idea for a specific scene making use of the Nintendo DS's interface.
Door To Before: From a narrative standpoint rather than one that you, the player, get to employ. Most of the numbered doors either return those who go through them to an earlier area or provide keys that unlock hallways in an earlier area. Most of the time the protagonists don't want or need to go to an earlier area, but it comes in handy a few times. Seven also applies doorjambs to a few areas specifically so he can backtrack.
It becomes a topic of conversation for the characters. They tend to find map pieces just after they're useful and realize, much to their frustration, that the rooms they've entered and exited are going to return them to the same place. Lotus and Seven are particularly Genre Savvy in this respect.
Downer Ending: There are six possible endings: two short bad endings, a decoy bad ending, the "true" bad ending (which must be finished before the actual True End can be unlocked), an aborted/To Be Continued ending that occurs if the player stumbles across the True End out of order (and it ends on a very sharp note), and the True End. The IOS version also adds a new bad ending. None of them are particularly happy.
The Submarine ending ends with everybody dead. Of course, Ace was acting. However, he would not have gotten the Q door, even with Lotus's and the 9th Man's bracelet. It's one of the three endings to have credits, making it the decoy bad ending. If you don't know that the Safe End is the bad end, the Submarine Ending seems the worst of all outcomes.
The Knife end has Ace getting Clover, Lotus, then Junpei with a short sharp metal implement. The fates of the others depend on whether Santa (who may have the gun) found out in time, and even then, it hardly matters: Akane will die and the Q door will remain locked.
Safe runs as if it were the proper ending, before taking a turn for It's a Wonderful Failure. After Junpei hits the Despair Event Horizon, Zero hands him a Plot Coupon and forces Junpei (and the player) to admit they made the wrong choices from the start. The ending name is a fandom pun to keep new players from becoming completely spoiled.
Axe has Clover taking a dive into the deep end, killing Santa and Seven over her brother's apparent death. Her justification over killing Akane was she was in her way, and then she kills Junpei For the Lulz. At the same time, Ace would have killed or kidnapped Lotus, and when Clover finds them... And she wouldn't have got the Q puzzle.
Coffin, the ending you get if you try to take the True End route out of order, leaves you with Santa taking June hostage.
Syringe, a bad ending exclusive to the IOS version, occurs if you go through Door 3. Junpei follows Clover after she runs off, and she stabs him with a syringe full of Soporil; he falls in the water around Deck D and drowns after succumbing to the drug.
The "True" Ending is, of course, an Earn Your Happy Ending. Although how happy it actually is is in the eye of the beholder.
On the True Ending path, Junpei and the others seem to pretty easily forgive the culprits once everything's revealed.
If Junpei goes through Door 3 (leaving Clover and Lotus behind to die just so he wouldn't be separated from June), all he gets for it when he returns is a glare and a slap on the cheek. Possibly justified, given that the team returned (subverting the "abandonment" part), they had found Snake, and they had just been through hell.
This is significantly changed in the IOS version, however. To be exact, it's completely averted. Instead of moving on to Door 2 and the Sub ending, Clover takes her revenge on Junpei via injecting him with Soparil and drowning him.
The Enneagram: Word of God says the nine characters were based on the nine character archetypes of the Enneagram of Personality. Specifically Ace is an Achiever (3), Snake an Investigator (5), Santa an Enthusiast (7), Clover a Loyalist (6), Junpei a Challenger (8), June a Peacemaker (9), Seven a Helper (2), Lotus an Individualist (4) and the Ninth Man a Reformer (1). Note that these are their Enneagram numbers and have no relationship to their bracelet numbers.
Everybody's Dead, Dave: the Submarine ending. Technically, all endings except the True End result in this, as Akane will die and the Q door will remain locked.
Everybody Lives: The best ending... except the 9th Man and two more of the Corrupt Corporate Executives...
Everyone Calls Him Barkeep / Being Watched: Early in the game, all the characters except for Junpei take a codename in case Zero just randomly kidnapped them but is keeping surveillance on them. Never mind that in most cases, they were probably carrying ID when kidnapped... Of course, if they'd all announced their names, Ace would have been clued in to Santa and June's true identity, Lotus's backplot, as well as Seven's story if his amnesia was an act. Which would have made Ace even more eager to backstab them, considering how quickly he moves against the 9th Man and Snake. Not surprising Aoi and Akane went along with the idea...
Evil Laugh: Ace, or rather, Gentarou Hongou, quite a few times actually.
An example is in the Knife Ending, when after discovering that Lotus' death had only happened recently, Junpei fails to realize the obvious and terrible reality that the killer is still there, since the floor they were on only had one entrance and exit (which was the same place) and that he just came out of the entrance with no one around.
Another example is the Axe Ending, where Junpei noticing Clover's sanity slippage may have stopped her from killing them.
FauxshadowThere are hints that this is all an experiment by Cradle Pharmaceuticals to make crystals or experiment with humans for mind-control for scientific advancement. Well. That's not totally off-track, but wrong Nonary Game. This one's motive is a lot weirder.
Feelies: If you pre-ordered from Gamestop online you got a replica of the bracelets. Thankfully it functions as a normal watch. Also, you used to be able to buy them for 5 bucks from the official store. Now they're collector's items that sell upwards of 200 dollars.
Final Boss: This game's equivalent to one... is a Sudoku Puzzle.
There are various Info Dumps on things like telepathy, synchronous "communication" between molecules, et cetera, foreshadowing young June transmitting her consciousness to present Junpei.
At one point, Lotus will show you a picture with black spots and ask you what the "photo" is supposed to be of. Then she will tell you a story about people doing an experiment by surveying a group of Americans about this picture. After a British radio show discussed the picture (Americans had no way to listen to this radio), scientists surveyed a different group of Americans and noticed that the percent who saw the picture correctly was higher than before, and then Lotus will discuss morphogenic resonance, or in short, telepathy. The funny thing here is that you can start the story over and re-answer the question.
On certain routes, the team finds a bracelet with the number zero. Upon experimentation, they discover it actually represents six (the letter "O" is the 15th letter of the alphabet; 15's digital root is 6—this is also a hint about another letter that resembles a number), foreshadowing the fact that Zero is actually June.
There's foreshadowing all over the place; one particularly subtle bit is in a Panty Shot gag of all things.
When the group is looking for Snake, Junpei can talk to Ace, and remark that he's surprised that Clover and Snake are siblings. Ace asks why, and when Junpei replies it's because they look so different, Ace says he supposes so. Ace has prosopagnosia; he had no idea they looked different. Additionally, Ace states that there are many siblings who do not look alike, foreshadowing the fact that Santa and June are siblings as well.
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 iron-plated windows slightly hint at the team not being on a ship at all; if they could see outside, the illusion would be broken.
Not too important, but when you look at the lights in the 1st Class Cabin, Snake looks surprised until Junpei clarifies where they are. Light is Snake's real name.
In the bad endings, you'll often come across another player who has just died, with the exception of "Snake" and the 9th Man, which cannot be prevented. If you've already gotten another bad ending, you'll probably realize that it won't be long for Junpei after that. This may be a result of June simply wanting to end that path since it didn't help her. Another subtle sign of bad endings are June's incinerator induced fevers and Seven's discrepancy-possible-false-memories.
Take a good look at June's bracelet on the cover. The upside-down 6 on her bracelet certainly looks an awful lot like a 9, doesn't it...?
In a bit of genius, during the safe ending you end up with the password 14383421, according to an interview with the director, he chose that number because if you multiply it by nine you get 129450789...the actual numerical value of everyone's bracelets.
The detonators not being real, except for the one in the ninth man, and possibly the one in Ace, is hinted at in a couple of places, specifically when Junpei observes that one of the searches for the DEAD felt like a lot longer than 81 seconds.
In the beginning of the game Junpei is talking about Zero as a he, then reconsiders, wondering if Zero is really a he or a she, which of course is foreshadowing of the real situation.
When choosing door , after Santa realizes Junpei's plan to go into the same room as June, and that he can't talk Junpei out of it, seems more intent than others on entering. June's bracelet is, of course, not , and Santa's bracelet is not  either.
The Coffin Ending has the same thing. The plan to send two groups of three through the doors would've sent Santa and June through separate doors, too.
The map Junpei finds of the bottom deck has a large part of its center burned away. Rather appropriate, considering there's a gigantic incinerator there.
Santa at one point says that you shouldn't trust anyone in the Nonary Game, because the person you trust most will turn on you. The person Junpei trusts most is Akane. She turns out to be behind the whole thing.
The flashback at the beginning of the game shows Junpei entering his apartment when he notices the window open. The narration says "Huh, did I leave that open?", except without quotation marks. Seeing how the second screen is June's POV...
When toying with the thermometer behind door number 3, Santa explains to Junpei that the reason thermometers stop at 107 degrees Fahrenheit (75 degrees Celsius) is because temperatures higher than that will cause permanent damage to the human body (comparing it to hard-boiling an egg) and that there is no point. He also explains that no disease would raise a fever to that high anyways. One would have to be forced into a super-heated sauna or incinerator to reach temperatures like that. June's on-and-off fever comes from being burned to death via Temporal Paradox.
There's various foreshadowing that Ace can't recognize faces due to Prospagnosia. Junpei himself notices and thinks to himself that Ace is acting strange.
Forced Into Evil: Zero, who is forced to run the second Nonary Game, as she previously foresaw its existence, and her life depends on information obtained from that foresight. She is fully aware that it's an evil act and tries to minimize the impact it has on innocent people, but is still forced to become a fugitive afterwards. If Junpei takes entirely the wrong path and disrupts the future game, Zero surprises the player with the declaration, "You misunderstand. You haven't lost... I have lost."
For Want of a Nail: A large number of 'nails' exist: every possible choice- from Junpei's travel partners to whether or not you take a bookmark- influences your fate. Akane is watching all of them, to find the best fate for her to follow.
A little toy doll, of all things, ends up playing a pivotal role in Akane's backstory. While escaping the first Deadly Game with Seven, she dropped it and ran back to get it...which led to her getting caught by the murderous Zero and getting thrown in the incinerator room...which led to her Traumatic Superpower Awakening...which allowed her to establish a psychic connection with Future!Junpei...which saved her life...which meant that, several years later, she had to trap Junpei, herself, and eight others in a similar Deadly Game so Junpei could connect psychically with Akane's past self, fulfil the paradox, and ensure her survival. If not for that oneimportant item falling at that one crucial moment, the entire game's events could have been averted.
Not related to the puzzles, per se, but the history and people behind the Nonary Game: Cradle Pharmaceutical's CEO Gentarou Hongou, who designed the project; Nagisa Nijisaki, Hongou's right-hand man and planner of the game; Teruaki Kubota, who developed the puzzles; and Kagechika Musashidou, who funded the project. Their experiment nearly kills several children in the process.
The Axe ending. Most of the group is murdered by Clover, who has bracelet number 4. It's also the only one of the four bad endings where the face of Junpei's murderer is revealed.
Alluded to when Santa mentions his dislike for the number four. In the English version, Junpei asks if it's about the Four Horsemen; clearly in the original he just thinks Santa is superstitious.
It is probable that the reason Santa hates the number four is that Snake uses four-leaf clovers in the first Nonary Game to encourage the other players to have faith, and by the end of the game his sister was dead.
Four is also the total number of bad endings (not counting the Coffin Ending, which is not really an ending at all so much as an acknowledgement that you were too smart for your own good and fulfilled the requirements for reaching the True Ending before the plot was ready to let you get there)
Four-Leaf Clover: The clover bookmark in second Nonary Game and nine clovers in first Nonary Game.
Freudian Excuse: The reason Ace, or rather, Gentarou Hongou gives for starting the Nonary Game.
Gainax Ending: Even the "True" ending qualifies as this, with 'Alice'.
Gas Mask Trenchcoat: Zero. And justified as Zero threw incapacitating smoke bombs at the players to kidnap them.
Gambit Roulette: Although admittedly being able to see the future, even if only once and when in mortal peril, gives a pretty good edge as to how to set up some of the crazier stunts Zero pulls - such as Snake's switcheroo, and knowing how and when Ace would react to "Snake" alone and seemingly confused.
Generation Xerox: Take one look at Nona and you'll immediately see her as a young Lotus.
Genre Savvy: Junpei can be this if you choose the right dialogue choices. He'll be this even if you don't — at worst, the other Nonary Game players will scold you for being foolish. Several other characters are Genre Savvy as well, chiefly —
Santa, who has done the Cold Equation, and warns you not to trust anyone. If you work with him more than once, he'll be the most useful member of your team when you're searching for a solution. Ultimately a double subversion, as he's Zero's assistant, and he's very familiar with the puzzles.
Gone Horribly Right: Ace, and the rest of Cradle Pharmaceutical, set up their Nonary Game for the purpose of getting people to tap into morphogenic fields, and control people. Ace in particular was extremely invested in getting them to tap into full sensory replacement. In the end, one of the children he kidnapped tapped into the fields perfectly. And she used that power to save herself from his twisted experiment, manipulate him (without using the fields on him) into killing his own accomplices, and ruin him financially and legally. The real twist of the knife is that she financed her revenge by buying stocks in Cradle. His own financial success funded his ruin.
Gorn: Meticulously detailed descriptions of exploded corpses, anyone?
Gory Discretion Shot: The game refuses to directly show you any of the exploded people, but to undo that, gives sickeningly detailed descriptions of the corpses in text. This doubles as a way to avoid a spoiler with the second victim, since if the corpse was shown any decently observant player might notice that its hair color does not match Snake's. Even with all the blood and half the head gone it would have been a dead giveaway that Snake was still alive.
Guide Dang It: One of the most common criticisms of the game was that the path to the true ending was very well hidden, practically requiring the player to make random guesses in order to find it. There are clues to the two routes you need to take, but it's equally possible to be Wrong Genre Savvy or Right for the Wrong Reasons when making decisions.
There are only four story checks that must be cleared to unlock the True End. If you play the game competently the entire time, you don't need to change your dialogue choices so much as line up the correct sequence of doors. All the choices you're offered while searching for Snake will have absolutely no bearing on the ending you receive, but if you don't know that, then the paths will seem hidden. The fact that the game greys out previously-used choices doesn't help, as it implicitly suggests that your prior choices were wrong.
The fact that even if you choose all of the correct doors and give Clover the bookmark, you still won't reach the True Ending if you didn't learn about ice-9 or didn't talk to Seven about it when he mentioned EDT. It really doesn't seem to have any relevance. The actual choosing of doors, there's only one split where one choice doesn't stand out as being the "most logical"—the 7-8 split. 4 is more logical than 5 because given which characters have already refused to go through the #5 door and which ones have volunteered, the only way to make the groups even in size would be to send June and Junpei through the #4 door with Santa and Lotus—and given the perceived danger, keeping the groups even seems wisest. It's the right choice. At the 6-1-2 split, the pairs that choose the #1 and #2 doors have digital roots of 5 and 6 respectively and could therefore go through their chosen doors with the addition of Junpei's 5, but the pair that chooses Door #6 has a digital root of 9; the group as a whole has a digital root of 7, so sending groups through the #1 and #6 doors is the only way to make sure everyone goes through a door. Combining these two truths makes Door #1 the "most logical" choice...and again, it's the correct one. There's absolutely nothing to point to Door #7 as being more logical than Door #8, however.
Also, the final puzzle in the torture room. Two switches each on two separate screens, each with three potential positions, and all four switches must be in the proper position to proceed. Unlike most times, there's no clue in the room as to what the proper configuration is, and because of the screen separation, you could have both switches on your current screen in the right position and not even know it because the switches on the other screen are wrong.
Guile Hero: Junpei, by making it so that he can get any result he wants in the door lottery.
He Knows Too Much: Ace murders the 9th man and the man he thinks is Snake to avoid his involvement in the Nonary Project leaking to the rest of the cast.
Snake is open about his blindness, but keeps the fact that he also has a prosthetic arm hidden.
Hollywood Hacking: Surprisingly averted. When a console needs to be hacked, said hacker writes a simple program to perform a basic but valid operation, namely brute-forcing the password. Unfortunately, programming does not work that way, especially on what is basically a DOS Prompt that is locked, but at least it refers to a real-world concept.
Junpei and June at the Saturn elevator, if you choose to assume the right (that is to say, wrong) reason for her nervousness. Doubles as Innocent Innuendo, but works better as this trope simply because of how long they go at it before Junpei realizes what June is referring to.
There's also a Too Funny to Be Evil dimension to this: it's unlikely you'd realize that's Zero you just had that conversation with!
Hurricane of Puns: Pick a door, any door. Chances are that you'll see at least one pun if you examine everything multiple times. Junpei, June, Clover, and Seven are the most major offenders of this trope.
Idiot Ball: Junpei can hold onto this firmly depending on the player's actions.
If Akane hadn't gone back for June (the doll) nine years ago, she never would have ended up locked in the incinerator all alone and the Second Nonary Game would have never been necessary in the first place.
Informed Deformity: Other characters keep commenting on how old Lotus is. She doesn't look old.
Innocent Innuendo: Besides the Saturn elevator example above, there's also the frozen chicken in the kitchen freezer beyond door 4. If Junpei examines it, June will say his "chunk of meat" is "really hard." Junpei will ask her to repeat the "really hard" part multiple times.
Interface Screw: You have to flip the DS upside-down for the final puzzle. This actually makes sense in-story, because all this time you've been playing as Akane 9 years ago, sending answers to Junpei in the present, with the top and bottom screens representing the two time periods respectively; this is the first and only time the situation is reversed.
It's Up to You: In spite of everyone working to escape the place, you're the only one who actually does any real work in the groups you're in. Granted, some of your teammates are more helpful than others. Justified by the fact that certain characters have to play dumb to certain puzzles, as they've seen them before. Only one character uses advance knowledge of the solution to sneak off.
Jerkass Has a Point: Lotus bringing up the fact that- for anyone to survive the game at all- people will have to be left behind, thus sparking conversation on who it will be. It was brutally pragmatic, but also necessary- nobody knew at the time that everyone could escape the game. She was just trying to solve a bad situation the only way she knew how. And given the tense situation they were in, it's perfectly reasonable that Lotus would want them to decide on who they'd sacrifice as soon as possible. Letting time pass would only make it worse.
Jigsaw Puzzle Plot: The fourth ending contains many plot-relevant revelations that are required to unlock the true ending.
There's also a track on the OST called "Imaginary" that seems to pop up whenever you're talking to June...
Lack of Empathy: Ace/Hongou. The problem might be related to his prosopagnosia: at a few points, he rants about how he can't really "see" people.
Let's Split Up, Gang: Forced by the way the numbered doors work (only three to five players can pass at one time). This trope is also played with and discussed — characters show reluctance to split up for fear of becoming even more lost.
Unfortunately, what's lost is a pronunciation pun, which is rather important during the climax of the True End, and makes no sense for the players unless they know Japanese. Specifically, the romaji letter "q" and the number "9" are both pronounced "kyuu" in Japanese. This also gives more meaning to the "Captain's Quarters," a door with a "q" where a witness is waiting for Ace to confess to his crimes; if he chooses to do so, he will be freed. An attempt was made to fix the most important part by changing it into a visual pun ( the instructions were moved to a card in Snake's pocket, and the number 9 does awfully like a lowercase letter q), but a Flashback towards the end of the game mistakenly shows the wrong thing, making most players forget that detail.
Junpei's deduction of figuring out how the authentication of the 'q' door works would make sense for a non-native English speaker, but a more simple explanation for a native English speaker is "Q is the 17th letter and its digital root is 8." The logic of the 'O' bracelet working as a 2nd 6 falls under the same logic; O = the 15th letter and its digital root is 6.
Love Transcends Spacetime: Junpei did not previously have a strong connection to the morphogenetic field, but still managed to awaken his potential to send and receive through the field to transmit the information needed to save Akane in the past simply through his bond with her.
Lucky Translation: Akane's Japanese alias is Murasaki (purple, from the 6th colour of the rainbow and her clothes), has nothing to do with June, her alias and the sixth month in English. Which makes Junpei's comment about as a child 'not seeing her after June' (the season), foreshadowing.)
Maiden Mother And Crone: The main female characters. June could be this trope all on her own, given how the game skips between time periods.
Clover is the Maiden. She's whimsical and emotional- intelligent but lacking in maturity. Lotus- apart from being a literal mother- is the oldest, and tends to treat the other players like they're children. Future!June/Zero is the Crone- she's manipulating everyone as fate dictates, and possesses knowledge both rare and mystical.
Moon Logic Puzzle: Averted, unusually for the genre. You may have overlooked an item and need to re-examine an area more thoroughly, but you'll be able to solve everything. This is actually lampshaded in the dialogue: in one of the endings, Lotus points out that the puzzles were always fair and never required resorting to instinct. The fact that the game runs itself is discussed in one narrative segment. You may want to keep a notebook close by, though, as some puzzles require memorizing multiple sequences of random data (e.g., compass directions) or translating letters.
Murder by Mistake: Ace's prosopagnosia results in him murdering Nijisaki, the decoy, instead of Snake. Granted, judging by the murder of the 9th Man partly being motivated by him knowing too much, he would have murdered Nijisaki, an accomplice in the Nonary Project, anyway.
Never Say "Die": When on the elevator with Junpei, June inadvertently fuels existing sexual tension by referring to dying as going to heaven instead.
New Game+: Upon beating the game for the first time, the game starts tracking which endings you've earned. You can also "begin with memories" which allows you to speed past dialogue you've already seen and dims choices you've already made in previous play-throughs.
Plot Time: Might as well list the whole index. Suffice it to say that your characters do things in exactly the amount of time they are allowed to get things done, no matter how long or how short a time it takes for you to solve puzzles, read dialogue, and walk around the ship.
Word of God states Junpei did not have any affinity with the Morphogenetic Field like the original 18 children prior to the Nonary Game, but managed to gain powers to access the field to transmit the solution for the last puzzle simply through his bond with Akane.
Also, Snake was able to withstand 6 bullets to the chest out of his love for his sister.
Purple Prose: The description of certain things tends to veer verbose.
Red Herring: There are several, the most major being Ice-9 and Alice. You still need them to reach the True Ending.
Red Oni, Blue Oni: This trope is used in almost every possible form, thanks to subverted stereotypes and numerous reveals. Some key examples:
Clover and Snake, with the colors to match. When Snake disappears, Clover's distress makes her become both onis, being alternately passionate and aloof.
Fridge Brilliance: Clover starts as a bubbly, energetic Red Oni, but becomes a cold and detached Blue Oni after believing her brother died (until she snaps, anyway). Snake, meanwhile, begins as a calm, erudite Blue Oni but after Clover dies goes completely berserk on a Roaring Rampage of Revenge.
Santa and June, whose names are homonyms for 'Blue' and 'Red' respectively. Santa's establishing character moment in the prologue would make him appear to be a classic Red Oni, but once all the pieces are collected and he drops the act, he seems to actually be the Blue Oni. June turns out to be the more emotional of the pair.
The game also makes more than one reference to red and blue creating purple, although one of these is Lost in Translation.
Refuge in Audacity: While in the series of rooms beyond Door 1, Ace pickpockets the solution to the puzzle from Junpei, goes into the next room while Junpei and Clover are talking, murders "Cap," and then slips back and puts the solution back in Junpei's pocket. And then, after finding the body and some information about "All-Ice," Ace suggests that the murderer was a defrosted mummy. Right.
Sequel Hook: Akane and Santa make a getaway in the True Ending, with Junpei and the other Nonary Game contestants chasing after them, setting the stage for a number of plotlines in Virtue's Last Reward.
Sequence Breaking: In-game, Seven puts things into the doors so they won't lock. These tend to be plot points.
Seven and Lotus, especially when they're the first ones to protest when they, at separate occasions, attempt to perform a Heroic Sacrifice. The excuses they come up with to explain their outbursts aren't very convincing either.
Various dialogues between Junpei and Clover in the Library and Cargo Room have this vibe. In the context of the events involving Clover that lead up to said rooms, Junpei giving her the laminated four-leaf clover bookmark and her glomping him when he inadvertently reveals that Snake is still alive, these moments can be read as Clover having developed a bit of a crush on Junpei.
Shoot the Shaggy Dog: Ending 5, where you learn very little of importance and are killed right in the middle of trying to figure out stuff. It is very confusing for both you and Junpei. Even the other "bad" endings give you more hope than this.
The safe ending can seem this, if you don't know that you need to get that ending first to reach the true ending.
June's reference to heaven ("I'll go to heaven") out of the blue whilst talking to Junpei about drowning (in the elevator scene) could allude to Ever17, where characters certainly drown and go to "heaven". Just a coincidence? The writer of Ever17 did lead the design team of 999...
Murder by way of explosives in a victim's stomach might be a reference to the memetically infamous "small bombs" theory. in Umineko no Naku Koro ni.
Shown Their Work: The Gigantic? That one's mostly real. It was to be the intended name of the third ship Britannic. William Thomas Stead is also completely authentic. The mummy, however, is a debunked legend, just Historical Fiction.
Six Is Nine: June's bracelet (a 6) actually being a 9, which allows her to open any of the doors in the game, making it an important hint to who Zero actually is.
Subverted since Snake makes this assumption and concludes that Santa has a number 0 bracelet when in truth June has 0 and Santa has 9.
And don't forget Santa/Aoi who does this after finding the charred remains of his sister. Of course, due to the Set Right What Once Went Wrong plot of the game he doesn't technically end up doing this.
Sneaky Departure: A villainous example: during the final puzzle, Present!Akane and Santa somehow manage to leave through the Q door without anybody noticing. (Admittedly, it helped that Junpei- the only one who fully realizes what's going on- is busy saving Past!Akane, and everybody else A.) Thinks they're about to die, and B.) Don't know that Akane and Santa are the villains.)
The Stinger: The very last scene.They've escaped the Nonary Game, and everyone is driving off through the desert, trying to make sense of everything that's happened...and then a strange, vaguely Egyptian, woman shows up in their path.
"It would not be long before Junpei realized who she was."
Take Your Time: All the puzzles aren't on a time limit and when people start talking they can talk a while. This gets kinda of silly when Junpei is locked in a flooding room or they're talking while freezing to death in a sub zero freezer. Apparently Talking Is a Free Action. Of course, it could be a clue that the characters aren't actually on a sinking ship.
In the incinerator room during the "True" ending, you only have 6 minutes left when you start working on the puzzle. That's 12 minutes of time wasted just talking, and seven minutes of that is of Junpei talking with past Akane.
Everyone takes up code names based off their number, except Junpei. Ace (1), Snake (as in "snake eyes," 2), Santa ("san" is "3" in Japanese, plus he's got a few stories about "Santa" to tell), Clover (4, like the leaves), June (The 6th month), Seven (which, uh, probably sounded cool and foreign in Japanese), and Lotus (8, like the petals on the flower).
The same applies in the Japanese version, where most of their assumed names either have the character for their number in them, or are similar in sound (again, except Junpei). Ace is Ichimiya ("ichi" is "1"), Snake is Ni(e)ls ("ni" is "two"), Santa is the same, Clover is Yotsuba ("clover" in Japanese), June is Murasaki (the character for "six" can be pronounced "mu"), Seven is... Seven, and Lotus is Yashiro (the character for "eight" can be pronounced "ya"). Mu can also refer to nothingness in both English and Japanese... that is, zero.
Averted in that Clover's name is actually Clover, well, Yotsuba.
Trial-and-Error Gameplay: The path to certain endings may seem like this at first, although more and more hints pop up as the game progresses. Plot-wise, the whole game can be seen as Young Akane experimenting with all of the story paths to see which one will lead to her salvation. Santa, behind Door 6, will discuss rats trapped in a flooding box and how, after enough repetitions, they figure out the exit from among seemingly arbitrary choices... hmmm...
Some of the paths make repeated references to "morphogenetic fields," the ability to transmit information between seemingly unconnected things. Morphogenetic fields are an actual phenomena - though it's very localized and revolves around discreet biochemical signals (and the shapes cells will conform to) rather than memories and image-sending. The game actually uses the concept of that name developed by Rupert Sheldrake (who is mentioned by name at one point when the concept is being explained).
Not to mention Ice-9 and the entire Alice incident.note Ice-9 is real, but the substance discussed in the game is a fictional element (inspired by Kurt Vonnegut) and Alice is a reference to the Urban Legend of the Titanic sinking caused by a mummy's curse.
Westminster Chimes: Used as a puzzle; you have to play the tune on a piano that's had its keys rearranged.
Yank the Dog's Chain: Meta-example. The colloquial name of the "Safe" ending implies that you will, in fact, be alive. No such luck... The term "Safe" actually refers to the safe that holds the letter.
You Wake Up in a Room: The game starts with your character waking up in the cabin of a large passenger ship. Of the nine characters involved, however, only one has amnesia and it isn't you. In fact, Junpei only needs a few minutes to get his bearings before the player sees exactly how he was abducted from his apartment.