Noein: Mou Hitori no Kimi e begins during the last summer of elementary school, when Haruka Kaminogi, Yuu Gotou, and two of their friends decide to undertake a test of courage at their local graveyard. Before the test begins, Haruka makes one last effort to pull Yuu away from his controlling mother, only to witness a strange fall of blue snow and the appearance of an imposing silver-haired man. A similar vision follows at the graveyard, where Haruka and her friends try to flee what they first assume are ghosts. In reality, the figures before them are Dragon Soldiers, an elite military group from the dimension La'cryma.
The Dragon Soldiers have traveled to Haruka and Yuu's world to secure the Dragon Torque, the entity they believe is their last hope for survival in a violent conflict across space-time. Their mission changes abruptly when both they and Haruka discover that the Dragon Torque is Haruka herself. As she tries to escape from the Dragon Soldiers, her closest ally becomes the same mysterious silver-haired man, Karasu, who claims to be another version of Yuu from fifteen years in the future. The series brings Haruka, Yuu, and the people around them into a war between dimensions in which La'cryma and the future itself hang in the balance.