The story follows Junpei, a college student who is abducted along with eight other people and forced to play the "Nonary Game", which puts its participants in a life-or-death situation, to escape from a sinking cruise liner.

999 was positively received, with reviewers praising the story, writing and puzzles, but criticizing the game's tone and trial-and-error gameplay.

An updated version of 999, with voice acting and higher resolution graphics, was released alongside a port of Virtue's Last Reward as part of the Zero Escape: The Nonary Games.

[3] These sections require little interaction from the player as they are spent reading the text that appears on the screen, which represents either dialogue between the various characters or Junpei's thoughts.

[4][5] An in-game calculator is provided for math-related problems,[6] and the player can ask characters for hints if they find an Escape room too difficult.

Zero announces over a loudspeaker that all nine are participants in the Nonary Game, explains the rules, and states each carry an explosive in their stomach that will go off if they try to bypass the digital root door locks.

Through various choices, Junpei learns of a previous Nonary Game, played nine years earlier, and the connections of the other characters through that, as well as studies about morphic resonance and stories of the Egyptian priestess Alice, who is frozen in ice-nine.

Junpei learns that the dead man was not Snake and that the first Nonary Game was run by Cradle Pharmaceutical, of which Ace is the CEO.

The surviving players confront Ace and deduce he killed every person found dead in order to both cover his identity and obtain their bracelets.

Junpei investigates a nearby room, and returns to find Akane and Santa have disappeared, after which he is knocked out by a gas grenade.

In the true ending, Junpei learns that the previous Nonary Game consisted of nine pairs of kidnapped siblings separated onto the ocean-bound Gigantic and in a mock-up in Building Q in a Nevada desert.

This Nonary Game went awry: Akane and her brother Santa were placed at the same location instead of being separated, and Seven discovered the kidnappings and rescued the children from the ship.

Unable to solve the puzzle, Akane was apparently burnt to death while the other children, including Snake and Lotus's daughters, escaped with Seven.

[10] After rescuing Snake, Junpei and the others reach the incinerator; Akane disappears and Santa escapes while taking Ace hostage, trapping the others inside.

Junpei realizes that Akane was Zero and, with assistance from Santa, had recreated the game and all the events she had witnessed in order to ensure her survival and avoid a temporal paradox.

As Junpei and the others escape, they discover that the game had taken place in Building Q the entire time; Akane and Santa have fled, leaving behind a car with Ace restrained in the trunk.

"; Uchikoshi researched it, and found the British author Rupert Sheldrake's theories of morphogenetic fields, which became the main theme of the game.

The theory is similar to telepathy, which answers the question of how organisms are able to simultaneously communicate ideas to each other, without physical or social interaction.

The characters were originally supposed to be handcuffed to each other as they try to escape, but the idea was scrapped as it was seen as overused, with appearances in light novels such as Mahou Shoujo Riska (2004).

[19] The Escape sequences were created to appeal to players' innate desires: Uchikoshi wanted them to feel the instinctive pleasure that he described as "I found it!".

The music was written using the Nintendo DS's internal synth, and Hosoe worked together with fellow SuperSweep composer Yousuke Yasui to make this less obvious.

Another challenge was getting the localization done in time: Nobara Nakayama, the game's translator, worked on it for 30 days, and the editing process took two months.

[36] A novelization of the game, Kyokugen Dasshutsu 9 Jikan 9 Nin 9 no Tobira Alterna,[d] was written by Kenji Kuroda and released by Kodansha in 2010 in two volumes, titled Jou and Ge.

[45] People who purchased the Windows version through Steam in its first week of release received a complimentary soundtrack, with songs from 999 and Virtue's Last Reward.

[53] Reviewers enjoyed the writing and narrative,[3][6][7][52] with Andy Goergen of Nintendo World Report labeling it as "a strong argument for video games as a new medium of storytelling".

[5] Zach Kaplan at Nintendo Life liked the dialogue, but found the third-person narration to be dull and slow, with out-of-place or clichéd metaphors and similes.

[3] Tony Ponce at Destructoid said that the characters initially seemed like a "stock anime cast", but that the player discovers more complexity in them after moving past first impressions.

He felt that the way the game favored textual narration over animated cutscenes made it more immersive, allowing the player to imagine the scenes.

[7] Kaplan called the presentation "awesome", saying that it looked great and that the artwork stood on its own despite the simplicity of the animations, and that the soundtrack was "fantastic".

[18] Zero Escape: Virtue's Last Reward, the successor to 999,[59] was developed by Chunsoft for the Nintendo 3DS and PlayStation Vita, and was first released on February 16, 2012, in Japan,[60] and later that year in North America and Europe.