The story takes place in Shinjuku City, Tokyo, where a series of mysterious disappearance incidents have been occurring. The protagonist, Win Kirifuda, woke up in this town half a year ago with no memories of his past. He spends his days feeling frustrated and out of place, unable to fit in at his high school or his part-time job, often passing the time at night in a park with a classmate named Niika. This aimless daily life is shattered by the arrival of a mysterious transfer student named Crysta, who claims to know everything about Win and further asserts that the two are engaged. However, a sinister and dubious presence lurks behind her, and the truth behind the frequent disappearances, Crysta's sudden appearance and goals, and Win's hidden past are all deeply interconnected. This narrative serves as an alternate time story that progresses parallel to the events of Duel Masters Win, depicting a never-before-seen world where Win has lost everything and is drawn into a battle to regain what he once desired.

The central figure is Win Kirifuda, a sixteen-year-old whose complete amnesia leaves him untethered from his identity. His life becomes intertwined with Crysta, a girl who holds the key to his past, and Niika, a classmate who provides a semblance of normalcy. The cast also includes Jashin-Kun, whose role is tied to the unfolding supernatural events. The setting is a modern and recognizable Shinjuku, but it is rendered strange by the escalating frequency of inexplicable vanishances, creating an atmosphere of urban unease and supernatural mystery.

The story unfolds as a dark mystery that leverages the established universe to tell a more mature and suspenseful story. The notable narrative arc begins with Wins amnesiac daily life and his frustrating search for belonging. This status quo is upended by the inciting incident of Crysta's arrival and her shocking claim of an engagement. The central conflict then shifts to investigating the truth behind the city's disappearances and determining whether Crysta is a guide to be trusted or a threat to be feared. The driving question is whether Win can recover his lost memories and understand his true connection to the chaos unfolding around him.