Makoto Naegi begins as an ordinary high school student unexpectedly chosen as Hope's Peak Academy's "Ultimate Lucky Student." Despite lacking an obvious exceptional talent, he possesses deep optimism and a strong belief in others, defining his character through inherent hopefulness.
Thrust into a deadly killing game shortly after enrollment, Makoto clings to faith in his classmates' inherent goodness despite betrayal and murder. Driven to uncover truth and protect friends, he actively participates in investigations and class trials. His sharp observation and deductive reasoning, not initially highlighted as a talent, prove crucial. Surviving the ordeal reinforces his core belief in hope and people's potential for positive change.
Joining the Future Foundation post-tragedy, Makoto ascends to lead its 14th Branch. His actions and ideology, prioritizing forgiveness and rehabilitation over punishment for those influenced by despair, spark conflict within Future Foundation leadership. This intensifies when Makoto protects former Remnants of Despair, believing in their redemption.
This choice leads a Future Foundation faction to label Makoto a traitor, resulting in his capture and imprisonment. Confined, he remains steadfast, refusing to compromise his belief in hope and redemption, voicing his resolve to allies like his sister Komaru.
During a critical confrontation, Makoto directly challenges Future Foundation acting chairman Kyosuke Munakata's rigid ideology of eliminating all despair sources, including the Remnants. Makoto passionately argues for a future built on hope and trust, believing people deserve second chances. His words and actions, alongside allies, prevent further bloodshed among Future Foundation members.
He plays a pivotal role in the final resolution by triggering the shutdown sequence for the Neo World Program, the virtual simulation holding comatose Remnants of Despair, facilitating their awakening and recovery. In the aftermath, Makoto works alongside closest allies sharing his vision to rebuild a world founded on hope and mutual understanding. His relationship with Kyoko Kirigiri remains significant. He is last seen actively participating in restoration efforts, embodying the hope he championed.