To reinforce the similarities between Nagito and Makoto, Kodaka had the characters share the same voice actors: Megumi Ogata and Bryce Papenbrook, and their names be anagrams of each other.

Critical response to Nagito's character was positive based on his ambiguous nature in Goodbye Despair where he often changes his personality, as well as his more comical take in the anime prequel Danganronpa 3: The End of Hope's Peak High School.

Komaeda's characterization was aimed to give players a confusing view in regards to Nagito's true self, based on the morally dubious and contradictory actions he committed over the course of the game.

[7] 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.

Kodaka was pleased with how Nagito was written in the anime, further comparing his school life and luck to the Rube Goldberg segment of the PythagoraSwitch educational television program.

After receiving a series of recorded messages from Nagito and proceeding to what appears to be Hope's Peak Academy, Hajime learns that Nagito, himself, and the others are in actuality computer avatar copies of the group known as the Remnants of Despair existing within a virtual reality created by the Neo World Program having been wiped by Makoto Naegi's Future Foundation offshoot in the hope of providing them redemption, despite being responsible for the deaths of millions.

[15][16] In Danganronpa Another Episode: Ultra Despair Girls, Nagito appears under the title of Servant (召使い Meshitsukai), serving under the Warriors of Hope who had captured him.

Following the defeat of the Warriors of Hope, the Servant carries away Monaca Towa, informing her that he will raise her to become "the second generation of Junko Enoshima" following her failure to have Komaru assume such a title.

The Servant makes a cameo at the beginning of the Future Arc, helping spread discord with the other Remnants of Despair after Junko is martyred, in his case by serving the Warriors of Hope.

[23] GameRant noted that there were multiple similarities between Nagito and Makoto Naegi which made several players confused to the point if they were related or even the same character especially because Ogata voices both of them in Japanese.

Though not made relevant in the plot, it is also noted that Nagito has romantic feelings for Hajime Hinata due to subtle hints he shows in free events and CD dramas.

[25] Reviewing the manga of Goodbye Despair, Anime UK News claimed that while Hajime is supposed to be the main character of the story, Nagito is more fitting for such role based on the behavior he demonstrates which makes him look "deranged than most" while also highlighting how different he is from his predecessor, Makoto.

However, the revelation of his dark self and skills when deducing murders in class trials made the reviewer claim that Nagito might be the most mysterious character in the entire game.

[29] Manga News felt that Nagito was an ambiguously evil person based on how often he tries to commit murders, most notably in the first trial when confessing he aimed to kill, but remains innocent as Teruteru made such action in his place.

The reviewer enjoyed the actions the character has performed not only in the game but also the Despair Arc anime from the franchise as despite his kind demeanor, his commentaries make Hajime become corrupted across the narrative.

[32][33] In a later review, the same writer from Manga.Tokyo called Nagito as one of his favorite characters, believing his calm demeanor and distinctive design make an interesting parallel to Junko Enoshima.

[34] Anime News Network enjoyed the encounter between Nagito and Izuru based on similar ideas like Manga.Tokyo but the felt this to be a form of fanservice that would appeal to players of Goodbye Despair as the two briefly interacted in Chapter 0 of the game.