Lu Chen transmigrates into the Naruto world, ready to leverage his foreknowledge to cling to powerful figures and enjoy a peaceful life. However, his plans are shattered when a mysterious System informs him that this reality is on the brink of destruction by eldritch anomalies. To survive, Lu Chen is forced to establish the Anomaly Containment Facility (SCP Foundation) and broadcast its existence to the entire shinobi world.

With a massive light screen appearing over the Five Great Nations, Lu Chen begins exposing terrifying containment files, starting with the plague-bringing SCP-049. As the Hokage, Kazekage, and rogue ninjas like Orochimaru witness descriptions of reality-bending horrors and undead surgeries, panic and intrigue spread instantly. While some view these anomalies as new threats to be eliminated, others see forbidden power to be exploited.

Lu Chen must navigate the chaos he creates, managing the reactions of the world's strongest ninjas while secretly building his organization to hold back the impending apocalypse. In a world of chakra and jutsu, the rules of science and horror collide.