[1] Writer Kazutaka Kodaka from Spike Chunsoft said in an interview that his aim was not to have players project themselves onto Makoto Naegi, a common method of writing for visual novels.

As time passed, Kazutaka thought of Makoto as a strong main character who can solve cases on his own, something he wanted to change for future games.

Originally, the team intended the adventure part of the game to be seen from a third-person perspective which would later be adopted for the spin-off Danganronpa Another Episode: Ultra Despair Girls.

[4] Localization member Robert Schiotis felt that finding a voice actor for the latter proved too challenging, as he is meant to clash with Makoto's ideals.

[8] In 2020, Kodaka revealed the anagram was used to engage fans of Danganronpa: Trigger Happy Havoc because of the lack of pre-release promotion materials for the original version of Goodbye Despair during its release year.

[13][14] In the original Japanese series, there is a scene in the finale where Nagito talks in joy while holding hand with Makoto, whom he declares his idol for their similar talents but is taken by his friends before he can finish their interactions.

Papenbrook added a line for Nagito that would come across comically as homoerotic to which Makoto would reply calmly in confusion and claimed he had fun for making his two characters had a talk.

[16] In the anime series, Shun Nishime took on the role,[17] and claimed his character was an ideal hero based on his actions presented in the high school scenario.

[6] Ogata found this type of characterization common in her career and compared Makoto to the "ordinary" mecha pilot Shinji Ikari from the anime Neon Genesis Evangelion.

The characters experience "despair" while they are trapped in the school and Makoto provides more emotional support to the cast across the story, giving the actress a far more optimistic message that the students are going to survive.

[23] Kodaka changed Kyosuke Munakata's sacrifice from script because he wanted Makoto to move forward carrying the burden of hope, elements often discussed by the cast.

After awakening in the school to find it in lockdown and a bear-like robot named Monokuma offering the 15 students trapped the right to leave if one among their number becomes "the blackened" and kills another without being found out by the other students at a subsequently held class trial and executed themselves,[25] Makoto is manipulated by his former classmate and pop star Sayaka Maizono into switching rooms with her to allow her to attempt to kill Leon Kuwata and frame Makoto for the crime.

Despite his disappointment at being manipulated by Sayaka, Makoto aims to solve the class trials and uncover each new "blackened" as more students decide to kill to escape,[26] assisted by Kyoko Kirigiri, who possesses keen observational and deductive skills.

[26] In an alternate ending to Trigger Happy Havoc in which Kyoko is executed after being blamed for killing the 16th student Mukuro Ikusaba, Makoto loses his will to fight in the next trials and establishes a polyamorous relationship with Byakuya Togami, Yasuhiro "Hiro" Hagakure, and Aoi "Hina" Asahina, with whom he has a child.

[30] In the spin-off Danganronpa Another Episode: Ultra Despair Girls, set between the events of the first two games, Makoto is depicted as an agent of the Future Foundation, dedicated to rebuilding society while searching for his sister Komaru.

However, they are imprisoned by a new Monokuma,[36] who forces everyone present to participate in a final killing game, while trying to avoid being poisoned to death by personalized forbidden actions.

Makoto is forbidden from running in the hallway, making him inactive;[37] Kyosuke orders his underlings to murder him, believing he is the actual culprit using Monokuma and filled with rage due to the first victim of the game being his close friend and lover Chisa Yukizome.

Upon testing the culprit's modus operandi, Makoto learns there is no killer and instead all victims committed suicide upon seeing brainwashing videos caused by Junko's pawn Ryota Mitarai.

Makoto remains unaware of the attack and his luck during the episode, after which point Junko decides to keep him alive as a "wild card", setting the events of Danganronpa: Trigger Happy Havoc.

[45] A virtual replica of Makoto additionally appears in the original video animation Nagito Komaeda and the Destroyer of Worlds dating Sayaka.

[46] Makoto makes minor cameo appearances in the light novel series Danganronpa/Zero, in which Ryoko Otonashi briefly encounters him while fleeing the Ultimate Bodyguard, the seventh volume of Danganronpa: Kirigiri, in which Kyoko Kirigiri meets him while attending Hope's Peak Academy, and the third volume of Danganronpa: Togami, in which he prepares Hope's Peak Academy for lockdown upon the commencement of "The Tragedy".

His luck led to the original female candidate intended for the role being replaced after unknowingly destroying her acceptance letter; a new lottery is held.

[56] The Danganronpa 3 incarnation of the character is also present in a collaboration with Hōkai Gakuen 2, a Chinese side-scrolling shooter mobile game developed by miHoYo for iOS and Android.

[63] Eurogamer said that Makoto highly contradicts the series' cast due to him not having any particular talent as he was chosen by luck but finds his journey painful to watch as the protagonist is unable to help other students who are in danger from being killed or becoming killers.

[65] Besides the serious class trials he solves, Makoto received attention from PlayStation LifeStyle and Polygon for his interactions with the main cast which allows them to be developed with them in the process.

[68] In a retrospective article, Yoneda in Inside Games was confused by the large amounts of similarities Makoto had with Nagito Komaeda voice actress included.

[70][71] Nevertheless, ReviewFix felt that despite his average appearance might result into looking down on, his actions when outsmarting killer during trials make Makoto comes across as the most appealing character.

[75][76] In the Gale Academic OneFile, David Eckstein-Schoemann noted that while Makoto is a common archetype the way, the anime handles him, makes him interesting to watch.

[85][86][87] In regards to the series' finale, critics felt the anime brought closure to Makoto's story properly based on his fate in the Hope Arc not only for his growth but also because he still continues his bond with the revived Kyoko.

[92] For the Danganronpa 3 anime, James Beckett from the same website once again praised Papenbrook for bringing "the goofy charm and charisma that has made Makoto such an endearing hero over the years".