Makoto has the title of Ultimate Lucky Student (超高校級の「幸運」chō kōkō kyū no “kōun”), though he appears to have both bad and good luck. Later, his title became Ultimate Hope (超高校級の「希望」chō kōkō kyū no “kibō”), due to his unusual optimism and ability to spread hope.
Makoto and the other survivors defeat the mastermind of the Killing School Life, Junko Enoshima in the final trial and escaped Hope's Peak Academy.
Makoto returns in Danganronpa 2: Goodbye Despair and Danganronpa Another Episode: Ultra Despair Girls as a member of the Future Foundation.
The DVD/BD vol.1 of Danganronpa: The Animation came with a 25~ page booklet called Makoto Naegi’s Worst Day Ever. This short story describes the chain of events that led to Makoto being selected as the Ultimate Lucky Student.
Makoto also appears in Danganronpa/Zero and Danganronpa IF.
Makoto returns in Danganronpa 3: The End of Hope's Peak Academy - Side: Future, attending his trial after he was charged on suspicion of treason for protecting the Remnants of Despair.
During the Final Killing Game, Makoto unknowingly triggers the NG Code of his dear friend, a survivor from the Killing School Life, and also his boss in the Future Foundation, Kyoko Kirigiri.
During the fifth time limit, Makoto becomes the "attacker" and doesn't kill anyone during the sleeping period, due to intervention by Juzo Sakakura. Along with four others, Naegi survive the Final Killing Game after Juzo deactivates the televisions by switching it to emergency power, causing the bangles to lose power.
After the events of Danganronpa 3, he becomes the new Headmaster of Hope's Peak Academy.