When designing the fangame's cast, creator LINUJ gave almost every character a basic "character motive", or in other words, an inspiration that drives their character:

• Yuki Maeda is "normal", "the main character that doesn't seem like one".
• Akane Taira is "someone who can cheer you up".
• Satsuki Iranami is a "mood-maker".
• Kakeru Yamaguchi is "a person who looks scary but is very nice".
• Kinji Uehara is "a benevolent priest".
• Kiyoka Maki is "a teenager girl".
• Teruya Otori is a "jerk".
• Kizuna Tomori is a "bitch".
• Mitsuhiro Higa is a "Spoiler:Chapter 1 killer".
• Kanata Inori is "an angel in white".
• Rei Mekaru is a "female [Byakuya] Togami" (a character from the official Danganronpa series).
• Haruhiko Koshibakawa is "a guy you would want as a friend".
• Ayame Hatano is a "healthy sports girl".
• Tsurugi Kinjo is "Spoiler:Light Yagami [from Death Note] without the Death Note".
• Mikako Kurokawa is "a mysterious girl".

The only two characters who LINUJ did not list character motives for are Spoiler:Yamato Kisaragi and Utsuro.

According to creator LINUJ, Tsurugi Kinjo's line of Spoiler:"Friend? Who is the friend you are talking about?" in response to Spoiler:"How are we supposed to stay calm… when our friend [Mitsuhiro Higa] has met such a horrible end?!" from Kanata Inori that reveals his truly psychotic nature was made up on the spot. Although LINUJ had planned for Kinjo's character motivation to be Spoiler:"Light Yagami [from Death Note] without the Death Note", the original line in this scene was Spoiler:"Everyone, we need to calm down. If we lose hope here, we won't be able to accomplish anything..." and he wasn't meant to hate evil to such an extreme extent. LINUJ later described this spur of the moment change as a "godsend in hindsight" and a pivotal change to the tone of the game's writing, as Kinjo's character would Spoiler:later be rewritten to go through an entire arc of alternating mental despair, which LINUJ described as: "everyone’s leader -> crazy, but still leader -> outcast -> mass suicide -> realization -> peak of despair".

According to creator LINUJ, he had initially forgotten to create Yuki Maeda's ahoge (which is typically a staple for Danganronpa protagonists) during the design process. He chose to keep it absent after noticing it could foreshadow Spoiler:the Yuki seen during gameplay being a decoy for the villain, Utsuro.

According to creator LINUJ, Kanata Inori was originally planned to be the Blackened student for Chapter 2, where she would have been revealed to be a crazy, psychotic person with her kind and sweet demeanor being nothing more than a facade. Instead, in the final game, Spoiler:Ayame Hatano is the second Blackened student, and Kanata Inori is one of the victims in Chapter 3.

According to creator LINUJ, he had originally planned to use Kakeru Yamaguchi more in the story, but he could not figure out how to use him without making him an intelligent character, and therefore making the game easier. LINUJ suggested that had Yamaguchi Spoiler:survived until the end of the game, he would not have fallen into despair at Utsuro's words unlike how Rei Mekaru, Teruya Otori, and Tsurugi Kinjo did.

Creator LINUJ's reasoning for making Danganronpa Another: Another Despair Academy was because he wanted more people to discover the Danganronpa series. At the time, visibility for the franchise in South Korea was low, and he didn't have the confidence or ability to translate a pre-existing game all by himself. LINUJ initially doubted he would be able to see through the development of the fangame, but that feeling slowly dissipated as he saw more posts from players enjoying new chapter releases on social media, motivating him to finish it.