A peaceful morning at the Tarikihongan Temple is shattered when a catastrophic surge of bugs infects Yggdrasil, the divine computer system that sustains all of Heaven and Earth. The crisis is triggered by the sudden death of Keiichi Morisato in a freak motorcycle accident, an event that reveals he has become a critical singularity within Yggdrasil due to his prolonged proximity to the goddesses. As Heaven evacuates and gods and goddesses begin to fade from existence in a chain reaction leading to Ragnarok, the three goddess sisters Belldandy, Urd, and Skuld execute a desperate and long-forgotten protocol: a system restore point for Yggdrasil, resetting the entire universe to the moment just before Keiichi first made his wish.

The restoration appears successful, but only the three goddesses retain their memories of the original timeline. Now living in a rebooted world where history is repeating itself, they must find a way to prevent the circumstances that led to the previous calamity. Belldandy, haunted by the knowledge that her close relationship with Keiichi contributed to the universe's collapse, makes the painful decision to keep her distance from him, even avoiding enrollment at Nekomi Institute of Technology where they first met. Urd works from Heaven to analyze the lingering anomalies, while Skuld uses her technical expertise to monitor for threats.

Despite their efforts, troubling signs emerge that the universe is trying to correct itself back toward the doomed timeline. An ancient sacred tree that Belldandy speaks with is dying, rejecting her divine magic. A malevolent ghost appears on the Nekomi Tech campus and specifically attacks Keiichi, revealing demonic origins. When Keiichi becomes trapped in a snowstorm while trying to return home with an engagement ring he purchased for Belldandy, the goddesses realize that fate is accelerating toward another catastrophe.

The situation grows more complex when Hild, the ruler of the Infernal Realm, arrives to explain the true nature of the crisis. The original system restore was only half completed, resetting Yggdrasil but failing to reset its counterpart Nidhogg, the infernal system. This incomplete restoration has created two diverging versions of reality, and the universe cannot sustain the contradiction. Hild reveals an alternate dimension where Belldandy never existed and Keiichi has a different life with another woman, demonstrating what is at stake.

In the final act, the goddesses join forces with Hild to perform a complete dual reset of both Yggdrasil and Nidhogg, fully reconciling the two divergent timelines. This time, the reset succeeds entirely, and while history begins anew once more, a small physical token of Keiichi and Belldandy's bond a ring crafted by Skuld survives the reset, offering hope that their connection will endure regardless of how many times the universe restarts.