Sixteen-year-old Win Kirifuda awakens in the Shinjuku district of Tokyo with no memory of who he is or how he arrived there. The city is plagued by a disturbing phenomenon where people suddenly vanish without explanation, and Win struggles to adapt to his new reality, feeling disconnected from his classmates at his new high school and his part-time job. His bleak daily routine consists of spending time with his cheerful friend Niika and others at night in a local park. This fragile existence is upended by the arrival of a mysterious transfer student named Krista, who claims to know everything about Win and declares herself to be his fiancée, though her true intentions remain unclear as suspicious shadows lurk behind her.

The story of Duel Masters LOST ~Bokyaku no Taiyo~ represents the third chapter of the Duel Masters LOST saga, following the events of Crystal of Remembrance and Reaper of the Moonlight. After acquiring a new Crystal Card, fragments of memory begin to return to Win. He recalls an image of a lighthouse from a photograph hanging in his room. As the true nature of the mysterious disappearances becomes clearer, it is revealed that a dangerous parallel realm called the Lost Field, a world teeming with dangerous creatures, is expanding and encroaching upon reality. Learning the location of the lighthouse from the photograph, Win resolves to travel there in search of clues to his lost past, accompanied by his loyal friend Niika and a new ally named Wayumi Tsukumoya.

The series deepens its exploration of the Lost Field, a boundary line that separates the human world from a dimension where creatures exist. Win is not alone in his quest, as he confronts the enigmatic Abyssbell = Jashin Emperor, a creature who observes the unfolding events with unknown intentions. A rival named Prince Kaiser also appears, manifesting as a phantom alongside the creature Bolshack Bacteras to challenge Win in a Duel, hoping to trigger his memories. The narrative follows Win as he journeys toward the lighthouse, seeking answers about the origin of the Lost Field, the truth behind Krista, and the meaning of his own forgotten identity.