The manga focuses on Kurisu Makise in the aftermath of the original Steins;Gate story’s climax. Following the cancellation of the final D-Mail that restored the Beta worldline, the narrative explores the days and weeks from her perspective, an angle largely unseen in the original visual novel or anime. The story specifically takes place on August 16th and September 21st, dates significant for their quiet devastation following Okabe Rintarou’s sacrifices.

The setting is a recognizable but emotionally altered Akihabara. Kurisu wanders the district, grappling with memories of events that, from her perspective, either never happened or exist only as faint Reading Steiner-like impressions. The manga expands on an audio drama of the same name, adding scenes such as a reunion with Faris NyanNyan and the other Future Gadget Lab members, exploring how the worldline shifts affected not just Okabe but everyone around him.

A major narrative arc delves into the tragic relationship between Kurisu and her estranged father, Shouichi Makise, known publicly as Dr. Nakabachi. Through flashbacks, the manga reveals that Shouichi was once a kind and eccentric father, similar in personality to Okabe, who formed a "Theory of Relativity Transcendence Committee" with his college friends. However, when a young Kurisu unintentionally disproved his life’s work, his pride shattered, leading to years of neglect and abuse. The story follows Kurisu’s attempt to reconcile with him, unaware that her desire to heal their relationship will lead directly to the fateful confrontation at the Radio Kaikan building where her death is fated to occur.

The narrative culminates in the revelation of why the worldline is so resistant to change. Kurisu’s father provides the emotional and scientific catalyst for the tragedy that defines the Alpha and Beta attractor fields. Unlike the original story, which follows Okabe’s struggle against "fate," this manga illustrates Kurisu’s acceptance of her role in the tragedy, highlighting her decision to trust Okabe even when she knows the likely outcome is her own death. The final arcs cover her perspective during the events of July 28th and her final moments, connecting directly to the opening scene of the original Steins;Gate.