After achieving the seemingly impossible task of altering timelines to save his friends, Rintarou Okabe finds himself plagued by an emotional burden and the haunting symptoms of his extensive time traveling. Despite the newfound peace and a semblance of normal life resuming around him, Okabe struggles with the psychological aftermath of his actions. The memories of countless timelines weigh heavily on his mind, isolating him from his friends who remember nothing of their shared ordeals across different realities. This isolation is exacerbated by his experiences of déjà vu, a disturbing side effect of his journeys through time.

As Okabe attempts to settle into his regular life, he suddenly vanishes from the world, leaving no trace behind. His disappearance throws his friends, particularly Kurisu Makise, into confusion and despair. Kurisu, who remembers Okabe due to their deep connection across timelines, becomes determined to find him and bring him back. Her quest involves delving into the complexities of time travel and facing the daunting task of navigating through the intricacies of their altered pasts. As she pushes against the boundaries of science and her own emotional limits, Kurisu finds herself racing against time itself to rectify the situation and resolve the paradoxes created by their time-traveling escapades, all while grappling with her feelings and the fundamental laws of the universe.