The story begins with the protagonist, Hattori Sakuraya, waking up in an unknown cave, unable to move or speak, experiencing a sharp pain. She struggles to recall how she got there, remembering a normal school day that led to a outing with her best friend, Otowa, and four other classmates to a trendy new cafe.
The narrative then shifts to the cafe outing, where Sakuraya's friends are excitedly discussing menu items and playfully bickering. Sakuraya, despite her outwardly stoic and expressionless demeanor, is internally thrilled about the cafe. Her friends note her usual lack of reaction, even to Otowa's affectionate gestures, but Otowa insists she can read Sakuraya's emotions. Sakuraya's internal monologue reveals her past: a prodigy due to her family's rigorous education, she became isolated due to her unusual abilities and later developed "anhedonia" after a childhood illness weakened her and intensified bullying. Otowa became her first and only friend, a beacon of warmth in her emotionally numb life.
Upon arriving at the cafe, the group orders various desserts. During their meal, Sakuraya's internal thoughts are interrupted by a sudden emergency alert from her "Smako" (a smart AI) and "Ailenses" (contact lens monitors). She reveals her secret identity as the daughter of a ninja father and a spy mother, equipped with seven spy gadgets. The alert indicates a bomb has been detected in the building. Sakuraya, unable to speak to her friends, manages to utter a single word, "Exit," which is misinterpreted as needing to use the restroom. Her friends, misunderstanding her urgency, help her move quickly.
As they are being evacuated, a panic erupts. Sakuraya and Otowa are separated from their friends. An explosion rocks the building, and it begins to collapse. In a desperate act of self-sacrifice, Sakuraya uses her "Tenshinki" (shape-shifting suit) and "Kurin" (levitation device) to propel Otowa to safety through a window, while she is crushed by debris.
Sakuraya awakens again, not dead, but as an infant in a strange, alien world filled with monstrous creatures. Her Smako AI informs her she is now a 0-year-old and that they are in the "Atlas Labyrinth." Despite her infant body, she can still activate her ninja abilities, "Ninki," and her spy gadgets, which have been integrated into this new world. She discovers her "Tenshinki" has manifested as the pink scarf Otowa gave her.
Sakuraya spends years in a safe zone within the labyrinth, honing her Ninki and adapting to her new reality. She learns to move and fight as a 5-year-old with the power of Ninki, her spy gadgets also having evolved. Driven by a sense of purpose and the feeling of being manipulated into survival, she decides to leave the safe zone and explore the dangerous labyrinth, facing formidable monsters and navigating treacherous environments. She encounters "Atlas-ticks," giant tick-like monsters, and uses her enhanced abilities to fight them. The narrative ends with Sakuraya facing a new challenge, determined to uncover the truth behind her transmigration and her purpose in this world.
