The story starts off with Junpei waking up in a ship, with no memory as to how he arrived there. On his wrist lies a bracelet with a single digit, "5", and on the door blocking his escape lies the same number. Suddenly, the window of his room breaks open, and water begins to flood the room. Junpei eventually escapes the room, but not before remembering how he got there in the first place. One night, after returning to his apartment, he was ambushed by a cloaked man calling himself Zero. Zero had said that Junpei was to participate in the Nonary Game, a game "where he would put his life on the line." Junpei could do nothing as Zero's paralyzing gas took over him.
Eventually, Junpei groups up with the 8 other participants of the Nonary Game, and in order to not reveal their identities, they each give themselves code names based on their bracelet numbers: Ace, Snake, Santa, Clover, June, Seven, Lotus, and 9th Man. Zero eventually tunes in and tells them the rules of the game: They must escape the ship within 9 hours, and must do so by going through a door marked with a 9. Additionally, the participants must also follow all of Zero's rules, else they explode from a bomb inside them. These rules are based off of the usage of numbered doors; around the ship there are doors marked with numbers, and only a group of 3-5 people whose digital root equals that number can pass. However, 9th Man chooses not to follow the rules, and ends up suffering the consequences. From here on out, it is up to the player to determine the path the story takes.
In truth, this Nonary Game is not the first one. The first Nonary Game happened 9 years ago, and consisted of two identical, but separate, locations: on a sister ship of the Titanic, the Gigantic, and in a secret facility in the Nevada Desert, codenamed Building Q. It was set up by four executives from Cradle Pharmaceuticals: Gentarou Hongou, CEO; Kagechika Musashidou, Majority Stock Holder; Nagisa Nijisaki; and Teruaki Kubota, Head of R&D. The purpose for this was twofold - to test the theory of Morphic resonance, which is reportedly affected by danger and epiphany, and to help the CEO of Cradle Pharmaceuticals, Gentarou Hongou, get over his prosopagnosia. The game placed pairs of siblings in the same life and death situations in different locations. Transmitters would solve puzzles and 'send' the answers to the siblings on the other side, the idea being that Morphic resonance works optimally under fear of death and through epiphanies. However, it didn't go according to plan. Unfortunately for Cradle Pharmaceuticals, a lone detective, who's codename in the Second Nonary Game would be Seven, who got captured trying to get onto the barge and save the children was placed in a room which had a vent leading to the incinerator in which the four remaining children unable to get through door nine were trapped in, and attempted to rescue the children. He almost succeeded, but one of the children, named Akane, accidentally gets recaptured by Gentarou, and locked inside of the incinerator. As the incinerator's timer begins to count down, Akane attempts to contact Junpei in the future with the use of Morphic resonance. She succeeds, and with Junpei's help, escapes the ship, along with those who would be later known as Santa, Seven, and Snake, as well as the daughter of Lotus, Nona and the other five children.
Nine years later, Akane, along with her brother Santa (and possibly Seven), recreate the Nonary Game, in order so that Junpei could be assured to have helped save Akane 9 years in the past. With Akane of the past's help in seeing the possible futures and relaying information from them to Junpei, it is eventually revealed that Ace is in fact Gentarou, and that 9th Man is Teruaki Kubota. Zero, who is really Akane and Santa, trick Ace into killing the other three executives in order to exact revenge on them for using them 9 years ago. Meanwhile, Snake, who Ace believes he has killed - he had done so because he believed Snake may have recognized him and wanted to take revenge himself - is trapped within a coffin. With Akane of the past's help, Junpei is able to release him. Eventually, Junpei, Snake, Lotus, Clover, and Seven find themselves trapped in the same incinerator Akane was trapped in 9 years ago. Junpei connects with Akane of the past, helps her escape, and then with her help once more, Junpei and the others escape the incinerator, thanks to the fact that the number on the door wasn't actually a 9, but a q (26), thus allowing them all to escape (5+2+4+7+8=26). Junpei and the rest of the group make it to the top of the ship, where they learn that they were never on the ship to begin with, but instead in the second building in the Nevada desert. With Akane and Santa ahead of them, they ride off into the desert in an SUV left for them, Ace tied up in the trunk. However, along the side of the road lies a familiar woman hitchhiking which has the same dress as the mysterious coffin woman "All-ice or Alice". The screen then fades to black and has the END at the bottom right corner of the touch screen.
However, this is only the True Ending. Depending on the player's decision throughout the game, other endings can ensue. In the Axe Ending, Clover, driven insane by her brother Snake's death, murders the rest of the participants with the axe used by Ace to kill Cap. In the Knife Ending, Ace murders Lotus and Junpei, and presumably, although not shown, the rest of the people as well. In the Submarine Ending, an unknown assailant kills everyone right before the group escapes on a submarine. It is presumed by several clues that this assailant is Ace. In the Safe Ending, which is required to unlock the True Ending, Clover is killed by Ace and Junpei discovers the truth behind Ace's evil deeds while on the ship. However, Junpei, having not rescued Akane in the past, is gassed by Zero after failing to be trapped within the incinerator. Zero says that it is she who has failed, as it is she who did not use morphic resonance correctly to get Junpei to be in that situation. Thus, Akane ceases to exist. It is worthy to note that these endings are not false, they are merely different future paths that Akane sees while in the incinerator. By seeing them all, Akane is able to feed Junpei various information, such as correct door selections, code combinations, and secrets about the characters' pasts, that he would have otherwise not known.
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