In addition to Uchikoshi, the development team includes character designers Kinu Nishimura and Rui Tomono, and music composer Shinji Hosoe.

The series was originally conceived when Chunsoft wanted Uchikoshi to write visual novels for a wider audience; he came up with the idea of combining the story with story-integrated puzzles.

While Nine Hours, Nine Persons, Nine Doors was initially planned as a stand-alone title, its success in the international market led to the development of two sequels, intended to be paired as a set.

Both Nine Hours, Nine Persons, Nine Doors and Virtue's Last Reward were commercial failures in Japan, and the third game was put on hold in 2014, only to resume the development for Zero Time Dilemma the following year, due to fan demand and the hiatus becoming big news.

[21] It does not include the additional story content that was part of the iOS version, but the final puzzle is different.

[23] A novelization of the first game, titled Kyokugen Dasshutsu 9 Jikan 9 Nin 9 no Tobira Alterna, was written by Kenji Kuroda and published by Kodansha in Japan in two volumes in 2010.

[32] Music albums with the soundtracks of the first two games were released by Super Sweep on December 23, 2009 and April 19, 2012, respectively.

Players had to solve real-life escape-the-room puzzles in the spirit of the Zero Escape series within a limited amount of time.

[5] During the Novel sections, the player reads dialogue, occasionally inputting choices that change the course of the story.

[36] The three Zero Escape games are narratively linked, with events of Zero Time Dilemma occurring between 999 and Virtue's Last Reward.

[42] Uchikoshi had initially written 999 as a stand-alone game, but its positive reception led to its sequels' development.

[43] The tension present in its first sequel Virtue's Last Reward was deliberately toned down from that in 999, as the results of a survey indicated that some Japanese people had not bought 999 because it seemed "too scary".

Uchikoshi stated that Zero Time Dilemma, the second sequel which was released in 2016, will "tone it up" in response to feedback from players who praised the sense of fear present in 999.

[43] While he intended for the series to be a trilogy with a story that ends on the third game,[43][50] he is open to "new incidents arriving" if fans still request it.

Uchikoshi examined the possibility of financing the development through the use of crowdfunding on a website like Kickstarter, but felt that the idea would not be persuasive enough for it to meet the goal; he also sought out opportunities with executives and investors.

[57] Among other influences for the series were writers Isaac Asimov and Kurt Vonnegut; Uchikoshi felt that 90% of any creative work consists of pieces from others' works, and that the remaining 10% is creativity, with the result being worthwhile hinging on how well a writer can incorporate their influences with their own ideas.

One thing he did to make the stories more believable was adding concepts such as Schrödinger's cat, which he felt added flavor and kept players wondering whether a particular concept could be the main idea of the game; he felt that when players wonder that, it makes the story feel more real, as they create the game world in their minds.

[42] He did not handle puzzle design himself, instead leaving a lot of the direction to other staff, and checking it multiple times.

While a lot of this had been taken care of by Spike Chunsoft, many parts of the game required different word choices in English depending on if a character knew of a particular thing or not; in these cases, the localization team had to track the story backwards.

Nakayama had started playing the game prior to starting work on the localization, but did not finish playing it until she was more than halfway through translating it; after learning that the plot hinged on a Japanese pun, they had to halt the localization, discuss it with Uchikoshi, come up with a solution, and go through the whole game to make sure that it still made sense.

[80][81] Uchikoshi noted that the positive reception of 999 from international fans outside of Japan directly influenced the development of Virtue's Last Reward.

[84] Several critics have praised the series' stories: Andy Goergen of Nintendo World Report commented on how 999 "truly expands what narrative video games can be capable of",[1] and Christian Nutt at Gamasutra said that Uchikoshi is "pushing the boundaries of what video game narrative can be".

[2] Tony Ponce of Destructoid called 999 "one of the greatest videogame tales ever told", and a great example of how engaging and powerful narratives in video games can be.

[37] Bob Mackey of 1UP.com featured 999 on a list of "must-play" Nintendo DS visual novels, citing its story and themes as being among the darkest on a Nintendo platform,[3] and called Virtue's Last Reward "one of the biggest, boldest visual novels to ever hit America".

[12] Jason Schreier of Kotaku included both 999 and Virtue's Last Reward on a list of "must-play" visual novels worth playing even for people who do not like anime tropes.

[87] Mike Manson of Nintendo Life and John McCaroll of RPGFan found problems with the controls used in the puzzle sections of Virtue's Last Reward.

[89][90] Austin Boosinger of Adventure Gamers felt that while the puzzles in Virtue's Last Reward were thematically appropriate, he thought they were "relatively uninspired in their variety" and that not many of them were fun or engaging.