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All hope seems lost when the world is suddenly invaded by aliens. Earth's only defense is a small three-person team known as the Special Counter-Aliens Task Force, consisting of an anonymous director, the tyrannical Shiro, and the easygoing Arikawa. The luck of the Task Force improves when Arikawa finds a teenage boy lying alone on a hill. The boy, Kakashi, is humanity's only hope—he has power previously unbeknownst capable of defeating the aliens! However, without any memories and with no knowledge on how to use his power, Kakashi is left clinging to Arikawa and Shiro as well as the only remnant of his previous life: his broken cellphone. Kakashi is conflicted by the fears and emotions clouding his mind and he calls his own motivations into question. Can he overcome his doubts and internal struggles and save the world?

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!

Rito Yuuki never gets a break—he's always finding himself in lewd accidents with girls around him. Although his heart still yearns for Haruna, his childhood love, Rito can't help but question his feelings for Lala, the alien princess who appeared in front of him and declared she would marry him. But now, it's not just Lala he has to deal with: her younger twin sisters, Momo and Nana, have also travelled to Earth, wanting to meet their older sister’s fiancé, and just as luck would have it, they end up staying at Rito's home. Meanwhile, amidst the bustle of his new family members, Yami, the human weapon girl, begins her pursuit for Rito. It's not an easy life for Rito as he deals with uncertain love, punishment for being a pervert, and a girl dead set on murdering him.

The anime centers on Minoa Asagaya, a new high school student in Sakaneko Private High School. Despite being a novice to anime, Minoa's classmate Arisu Kamiigusa invites her to make an "anime research club" at school. Through conversations with her classmate Miko Kouenji, as well as various anime-loving upperclassmen, Minoa gradually gets hooked on anime. While they stand against the student council's continuous efforts to disband their club, and they ignore the impending end of the world, they talk about anime, whether in Akiba, or in real-life "sacred place" anime settings, or the hot springs.