Takashi Natsume and his spirit companion Madara, nicknamed "Nyanko," continue returning the names of spirits from the Book of Friends given by his late grandmother Reiko Natsume.

On his way back from school one day, Takashi encounters a lurking spirit named Monmonbou, who recalls memories of Takashi's grandmother after hearing his name. Takashi's natural curiosity leads him to explore a mysterious town where his grandmother used to live. Befriending her old acquaintance Yorie Tsumura and Yorie's son Mukuo, Takashi unveils more of his grandmother's past.

In the meantime, Nyanko detours for food and stumbles upon a suspicious "Spirit Seed," which miraculously sprouts into a fruit tree overnight. Giving in to temptation, Nyanko consumes the fruit, splitting him into three. Seeking a solution to Nyanko's predicament, Takashi and his friends lend a hand, unexpectedly uncovering more secrets the town holds in the process.

[Written by MAL Rewrite]

The year is 1863 and as Japan's long festering wounds of political discord erupt into violent waves of street clashes and murder, the Tokugawa Shogunate sends a new force of masterless samurai called the Roshigumi to the aid of the Aizu forces in Kyoto. However the new "police" are anything but a cohesive force and assassination has already split them into two opposing factions. The stronger is led by the brutal Serizawa Kamo and the lesser by the more honorable but less assertive Isami Kondo. It is into this pack of wolves that Ryunosuke Ibuki is dragged by the rabid Serizawa. Forced to be a virtual slave by blood debt, he hates the samurai and everything they stand for. But as he sees how the other half of the samurai live, he begins to believe that there may still be a chance, for both himself and Japan, if only Kondo will step up and take down the mad dog Serizawa!

Because of a mistake in the summoning process, 30-year-old social animal Liu Yinuo was accidentally summoned into the game world. In order to return to reality as soon as possible, Liu Yinuo began to assist the 18-year-old "brave" Tian Enya to save the world. With his excellent cognition, Yinuo, who was originally a high-player, was like a duck to water in another world. Enya also grew from a wayward little girl to a mature and reliable big girl.

Shin Hazama has shut his heart ever since the mysterious and sudden death of his mother during his childhood. With his scientist father occupied with research, he can only rely on his childhood friend, Kotori Izumi, the popular and good-natured daughter of his father's employer. At the end of their third year of high school with graduation right around the corner, Shin and Kotori finally begin to move forward together, both in life and in love. Everything falls apart again when Shin's father also suddenly dies. But before things can settle down, he and Kotori learn the secret behind his parents' sudden deaths when they encounter agents from a high-tech dystopian Japan existing in a parallel universe. Among them is Jin, Shin's "relative self," who is working against the humanoid weapons Miko and Niko. As the lives of relative selves are linked, Jin has two objectives: defend the vulnerable Shin to protect both their lives, and assassinate Kotori to end the ironclad rule of her relative self, Princess Kotoko—his mortal enemy and the killer of his parents. Confronted with this new reality, Shin and Kotori must honestly face their feelings for each other, even if the world as they know it will end tomorrow. [Written by MAL Rewrite]