Yuno Gasai lives a normal life as a first-year in high school. She gets along well with her parents and even has a small circle of friends. However, she cannot help but feel as if someone is missing from her life, someone so important to her that it was as if she had lived another life trying desperately to stay with them. After a class trip to the beach, Yuno returns home; but in the middle of the night, she receives strange messages from a voice only she can hear. The voice informs her of the person she is desperate to meet and that she must find him. Soon, she finds herself in a mysterious realm, her only goal being reunited with the person she cannot remember. Though obstacles stand in her way, Yuno will stop at nothing to meet her beloved once again.

Makoto Hanaoka, a womanly second-year student, easily attracts other people's attention. First-year student Saki Aoi is no exception, and she falls in love with Makoto at first sight. Having a vibrant and vigorous personality, she does not hesitate to confess her feelings to her senior. However, Makoto differs significantly from the person Saki perceives: Makoto is not a girl, but rather a cross-dressing boy! After revealing his well-known secret to Saki, Makoto expects her to be disgusted. Surprisingly, she is instead captivated by this revelation. Nonetheless, he still rejects her, but Saki's determination does not stop her from declaring that she will become his first love. With Saki and his childhood friend at his side, Makoto's world brightens, giving him strength amid his struggle between his interests and the expectations placed on him.

Haruto Kirishima lived a calm life out in the countryside, away from the fast-paced life of the city. Then Yuzuki Eba appeared in his life out of nowhere, having come from Tokyo to briefly live with her family. Their time together left him enamored with the memories of that short period before she just as abruptly disappeared from his life, and left him full of questions. Kimi no Iru Machi begins some time later, after Haruto moves to Tokyo to live with his sister, in order to pursue a career as a cook. In reality though he wishes to be with Yuzuki. Things don't start good though. When he arrives he is mistaken for a burglar and attacked by his sister's neighbour Mishima Asuka. After the misunderstanding is cleared his feelings begin to waver though. Is Eba, who keeps avoiding him for seemingly no reason, the one for him or is it Asuka?

The dispassionate, transforming assassin Golden Darkness returns to peer deeper into the mysteries surrounding her new life, while a sinister Nemesis manipulates her younger sister Mea from the shadows. Along with their newly discovered mother, Tearju, this previously estranged family quickly becomes the center of everyone's attention. On the other hand, Princess Momo's Harem Plan stands on shaky ground amidst Rito's inability to confess to his longtime crush Haruna, who has grown feelings of her own. But things aren't as peaceful as they seem; an evil force looms amidst the innocuous commotion, threatening to eclipse the love, happiness, and friendship of Rito and his harem. Only the light of love can hope to banish the shadow. [Written by MAL Rewrite]