In the DS and The Nonary Games versions of Zero Escape: Nine Hours, Nine Persons, Nine Doors, there are six endings, although only one of them is canon (The True Ending). Because the Safe/Zero Lost Ending is required for the True Ending, the Safe/Zero Lost Ending can also be canon in another timeline/universe. The Safe and Zero Lost Endings are the same ending; the DS version uses Safe while The Nonary Games uses Zero Lost.
In the iOS version of the game, a new ending (syringe) was added, creating a total of seven endings.
The endings are in descending order (6 to 1), with the iOS' additional ending at the bottom. The ending received is determined by the numbered doors that Junpei goes through, as well as his answers to certain questions.
This ending is achieved by going through Door 2 on any route. It is advised to take Door 3 first, since it has no branch routes. However, this does not apply to the iOS version, as taking Door 3 on any route would lead to the Syringe Ending.
In this ending, Junpei, Seven and Lotus complete the puzzles beyond Door 2 to acquire the Sun Key, and quickly hurry back to the central staircase on C Deck to open the Sun Door. However, as soon as they arrive, they find the motionless, blood-covered bodies of Ace, Santa, and Clover strewn along the central staircase.
Seven verifies that Clover no longer has a pulse, but not the other two because Lotus steals the Sun key from Junpei's pocket. She begs them to head through the Sun door, afraid that the murderer might return soon. Junpei then glances at the corpses on the stairs and starts to think that June, who was not among them, is responsible, but he states that he doesn't want to think about that possibility.
Beyond the somehow already unlocked Sun door, then through an odd automatic door, Junpei is horrified to discover a dying June, and breaks down after witnessing her final moments.
Afterwards, he notices Seven and Lotus missing, looks for them, and discovers they've been murdered as well, back outside the automatic door.
Mentally and emotionally broken at this point, Junpei mindlessly stumbles to the submarine, where he is stabbed in the back. He falls in the submarine pool, unable to catch a glimpse of the assailant. The scenes of the 9 players' deaths run through his mind starting with the 9th Man and ending with Junpei. He sinks deeper into the water, asking who had killed them all, until everything fades to black.
Regarding the killer, Ace faked his death and is confirmed to be the culprit. Lotus' missing bracelet was a hint leading to Ace, since he goes after it in almost every other ending in order to help him pass Door 9. The blood under Ace is there to make Junpei, Seven, and Lotus think that he was killed. Presumably, he moved the other bodies from the blood and laid in it. Although this ending displays the brutal murders of every character, Snake is actually exempt, and would probably remain in the coffin and eventually die from the lack of oxygen in the coffin.
You achieve this ending by going through Door 6 without actually following the Safe Ending path, meaning that this ending is only achieved by going through either Door 4 or Door 7, or both. In other words, there are three possible ways: Doors 4 > 7 > 6, Doors 4 > 8 > 6, or Doors 5 > 7 > 6.
In this ending, the team that went through Door 6 (Ace, Santa, Junpei, and June) find the chapel with the two 9 doors. However, the team that went through Door 1 return without Clover, which begins a search for her. After searching for Clover in the large hospital room, Junpei and June decide it would be best to split up to cover more ground. However, before they go, Junpei thinks about himself and June and how he used to call her Kanny.
After a little flirting, they split up and Junpei heads to E Deck to continue his search for Clover. While on E Deck, Junpei finds a dead Lotus. After mourning her death and realizing someone took her bracelet, he is stabbed in the back by Ace (confirmed due to other endings). Ace goes back after collecting Junpei's bracelet, presumably to kill the others.
People may get confused on this one because the survivors could restrain Ace, since he only has a knife. But in the Safe Ending, he is shown to have the golden revolver. Players can also combine this ending with the Axe Ending, which could happen due to similarities on Clover's attitude, but none of this is revealed, since Junpei dies rapidly. This is one of the endings that can lead to the freedom of Ace alone, should he get the "sinister hand" tip, freeing Snake, murdering him, and getting to Door q, eventually passing through by trial and error. This is the only ending that doesn't show what happens to June, although it is assumed that she dies because Junpei would not be able to save her in the incinerator. This ending is also the only one that Junpei sees the killer, but does not say who it is, as he is unable to think clearly while dying. This ending is recommended to be done before the Safe and after the Submarine. The Axe Ending complements this one in a manner, so it's up to you which one to do first.
Safe/Zero Lost Ending
This ending is achieved by going through Door 5, then Door 8, and finally Door 6. There is no other way. In this, everything is the same as in the Knife ending, but Clover's body is actually found in the 1st class cabin bathroom, holding the "sinister hand" paper and the 0 bracelet from the Captain and Lotus is not killed by Ace. Also the romantic scene with Junpei and June does not occur. This grants access to the Cradle Pharmaceutical secrets in the safe, in the same room with the names of the four masterminds behind the First Nonary Game, plus Zero's revenge plot. The note says that Snake participated in the First Nonary Game.
Junpei then realizes who the killer is. He brings the other five remaining players to the Large hospital room. He has Ace, Lotus and Seven scan their bracelets on Door 3 via their palms, Junpei then waves his bracelet over the RED, and beeps with Junpei able to open the door. Junpei reveals you don't need to place your hands on the scanner panel to activate the RED but merely using the bracelet works as well.
Junpei then asks Ace who he is. Ace says he's Junpei, but Junpei says he is Santa claiming they swapped clothes. He asks Ace why he thinks Junpei is Junpei and he says because if he was Santa, Door 3 wouldn't open. Junpei capitalises on this, calling it strange, and reveals Ace has Prosopagnosia, which he reluctantly admits.
Junpei believes that Ace is the killer, and tells him there are three pieces of evidence to support this. The first, Junpei states that Ace used Soporil on himself on purpose in order to prevent the others from going through Door 3, which would reveal the death of "Snake". Ace denies this and says he was just acting altruistically. Junpei argues that he knew that the doors would lead back to the hospital room, but Ace denies this as well.
Junpei then reveals his second piece of evidence: he believes the killer has Prosopagnosia because he killed Nagisa (who Junpei calls Guy X), who was wearing Snake's clothes. He states that someone who could differentiate human faces wouldn't make the mistake Ace did. He reveals that Clover told him Snake had a prosthetic left arm, and that the bone in the left arm Guy X's corpse in the shower room was exposed. Ace states that he has no motives, but Junpei says he has two motives. The first being that Snake knew about Ace's past and the second being that Snake had a grudge against Ace due to the First Nonary Game, and that he might strike back. Santa asks what the grudge was and Junpei shows him the paper he got from the safe. He reads part of it which says that the person with the number 2 bracelet played before and that it was organised by Gentarou Hongou. Ace says he was being framed, and Junpei uses this to his advantage, saying Ace's real name is Gentarou Hongou. Ace admits he is Gentarou Hongou, CEO of Cradle Pharmaceutical, but denies knowing anything about the Nonary Game.
Ace asks how he could have killed Guy X, saying he could do it on his own, but Junpei says he could of and puts his hands in his pockets saying he took something of Ace while he was unconscious. On instinct Ace puts his hands in his pockets, and Junpei smiles, his trap working and reveals Ace has the number 9 bracelet. He explains that he could have used his own bracelet along with Guy X's and the 9th Man's to open Door 3.
Ace then laughs, admits he is the killer and that he took the knife and Bracelet 9 from the First Class Cabin and then killed Guy X and that he is also the killer of Clover, as Ace was worried Clover found something in Door 1 and that Snake might have told Clover something. He admits to being defeated by Zero but not by Junpei. Lotus then punches Ace, who grabs her and puts a gun to her face, which he obtained from Door 6. He then admits to being the killer of the 9th Man, by tricking him into believing the DEADs were modified and going into Door 5. He explains his motives, being that the 9th Man knew Ace, to obtain the Number 9 bracelet as it is an important number, and that he wanted to see if the Nonary Game was a joke or not. He then leaves for Door 9.
June suffers from her fever and stays in the large hospital room with Santa. Junpei and Seven reach the funeral room only to find a fleeing Ace. Junpei hears a bumping in the nearby coffin and, using the "sinister hand" tip, frees an oddly-clothed Snake.
They proceed through Door 9 using the 0 bracelet (which is actually of 6 value, being that O is 24 in base-10, 2+4=6). Finding the incinerator room with Ace and Lotus, Ace reveals his evildoings to Snake, who goes on a rampage against his nemesis to avenge Clover's death. Ace wastes all six of the golden gun's bullets on Snake, who holds him in the incinerator until they both burn alive.
Junpei, Seven, and Lotus manage to escape. Junpei goes to fetch the other two, but finds an unconscious June on the ground. Zero contacts him, saying that he (Zero) lost the game. A gas grenade appears and knocks Junpei unconscious.
This ending is necessary in order to get the True Ending, due to past Akane's morphic resonance on the "sinister hand" tip. One of the most confusing endings and by far the most neutral one, we don't know what happens to Junpei after he talks to Zero, what happens to Seven and Lotus, and what happened to Santa. Since it's later revealed that Santa is Zero's assistant, there is little to no reason for him to leave June. There's a possibility that Santa returned Seven, Lotus, and Junpei to their regular lives after knocking them out at the end of the game. This ending is best enjoyed being your second to last one, just before the True Ending. The revelations on Ace's story can affect the next endings heavily.
This ending is achieved by going through Door 1 and not following the True Ending path.
In this one, after the discovery of Door 9, Clover insists in going through Door 2 with Santa, June and Seven, saying that they may find another exit. While the others wait, Ace has a private talk with Lotus, and either threatens her, kills her, or convinces her to go with him to Door 9, since he has the 9th Man's bracelet and three players (or bracelets) is the minimum to open a door. 1 + 9 + 8 = 18 = 1 + 8 = 9.
Junpei is left alone, when suddenly, only Clover returns, with the others' bracelets in her possession, including the 0 bracelet. She reveals that she calculated who killed her brother Snake in Door 3 (Santa and Seven, 2 + 3 + 7 = 12 = 1 + 2 = 3) and decided to murder them for the murder of Snake. Clover also killed a defending June because she "got in the way".
She offers her hand to Junpei, since they can go through Door 9 together (4+5+0= 9). Junpei accepts the offer, even after experiencing the mindcrush of Akane's death, only to get chopped in the neck by the axe that was in the Captain's Quarters. Clover walks toward Door 9 as Junpei watches her sickening grin while dying and bleeding to death on the floor.
This ending is the only one that has a presumable end, since Clover would either find and kill Ace and Lotus, or proceed to the incinerator after them. It is also unknown if Clover finds out Snake is alive and how she would react to him surviving and dealing with the fact that she killed three innocent people, since she would not find out June was Zero.
The director himself said that he "didn't believe Clover made it out" in this ending. It is unknown if Clover survived in the incinerator because of the puzzle and the door really being Door q instead. Considering the value of the 0 bracelet given in other endings (it is actually 6), Clover would have problems when facing door 9, because the bracelets she thought she had (4+5+0=9) have in fact a different digital root (it would be 6 as 4+5+6 = 15, which leads to 1+5 = 6).
This ending is also the most confusing one, as the player would likely suspect that Clover was the killer. Also, it could be possible that Ace manipulated Clover into killing Seven, Santa, and June to increase his chances of escape. However, if the two were to fight, Clover would win. She has an ax while Ace has a knife, making Clover the most probable winner. There is also the possibility of Clover having acquired the golden revolver from Santa, since he took the revolver from the coffin in the cargo room, but it is not certain if she did so.
This ending also shows how the mental stress of the Nonary Game can lead a player to go insane.
This ending is deemed unnecessary because obtaining the True Ending will also activate the clear icon for this ending. Though some players believe that this ending can be fun to make your first or second since it might intrigue the player, and leave them suspenseful in waiting for the True Ending.
To achieve the coffin ending, one must follow all of the steps below for the 'true' ending, but not yet have completed the Safe Ending. The ending follows like the True Ending, but stops just before Junpei opens the coffin, as he doesn't know how to figure out the numbers for the coffin's lock. The "To be continued" screen appears then appears, and he hears a mysterious voice say "Truth has gone".
A player who gets this ending (and is unspoiled) would likely presume that the being inside the coffin was All-ice.
You cannot get this ending unless you have gotten the Safe Ending first. In order to obtain the true ending, one must go through Doors 4, 7, and 1, along with answering certain dialogue options to certain characters. These options include accepting the four-leaf clover bookmark from Santa in Door 4 and eventually giving the bookmark to Clover in Door 7, as well as asking Seven about Ice-9 (and thus learning about All-ice) in Door 7.
In the true ending, Junpei slowly uncovers the truth about everyone participating in the Second Nonary Game. Junpei also discovers that the players in the Second Nonary Game are connected in one way or another to the First Nonary Game and also finds out who was involved in the First Nonary Game. Those involved during the first Nonary Game were Ace, Snake, Santa, Clover, June, Seven, Lotus's twin daughters and the 9th Man. The reason why the Nonary Game was created was to allow Ace to tap into the morphic resonance field so he could cure his prosopagnosia.
Throughout the game, Seven will regain some of his memories and will tell Junpei about how he used to be a detective and was onto Ace before getting caught by his men and thrown into a cell. Junpei not only discovers Seven's past and how he tried to help save all the kids playing the Nonary Game, he also finds out that his best friend from childhood, Akane, died after being locked in the incinerator by Ace in an attempt to escape. During the play through however, Junpei eventually finds out that he can save the Akane of nine years ago by tapping into the morphic resonance field.
Little does anyone know, Akane has been tapping into the morphic resonance field throughout the entire game telling Junpei information about the past Nonary Game. Everyone questions Junpei as to how he knows the information he does and never does he have an answer until the end of the game when he realizes that Akane has been looking through his eyes and planting information into his thoughts. Realizing Akane of the past is trying to talk to Junpei and help him, he guides her through a Sudoku puzzle and, in turn, helps her and rewrites the past by saving her.
Before Junpei saves her, he starts to reminisce on his childhood with Akane and the memories they shared together. Once Akane is saved, the door in the incinerator opens and the remaining players (Snake, Clover, Seven, Junpei and Lotus) all escape and find themselves on top of a building, which is Building Q.
After leaving the roof of the building, with Ace in the back of the car, Clover drives the gang away into freedom. While in the car, Junpei asks Ace and Seven about All-ice. Before the game ends, Junpei and Seven notice a hitchhiker on the road. The hitchhiker on the road is actually Alice. Clover stops the car to let her in.
Exclusive to 999: The Novel for iOS, this ending is reached by going through Door 3. After Junpei, June, Seven, and Santa escape from the Shower room, they go back to the large hospital room. Lotus slaps Junpei for leaving her and Clover behind. Seven then tells Lotus and Clover to see what is behind Door 3, Ace going along with them. After seeing the corpse behind the door, Seven states that Snake might have been murdered. Clover suddenly screams that she will never forgive the killer and threatens to kill him and suddenly runs off.
Junpei chases after her and winds up near the central staircase leading down to D Deck. Clover injects him with the Soporil-filled syringe she presumably took from Ace. Junpei falls into the water and Clover tells him to take her hand. He realizes that Clover might have injected him because she thought he was the one who killed Snake and that his death may have caused her to lose her mind. He tries to reach for her hand, but she refuses, saying that she would never help him. Junpei drowns after succumbing to the anesthesia. Clover's expression on this ending is the same as the one of her from the Axe Ending. Everything that occurs in this ending is the same on the DS until Seven speaks to the remaining players about "Snake's" death.