Ayakashi are strange, supernatural creatures invisible to the majority of people. Though most are harmless, some ayakashi attack humans to devour their life force. Exorcist ninjas are tasked with protecting people from these spiteful spirits. Matsuri Kazamaki is a young exorcist ninja born to a prestigious clan. His childhood friend, Suzu Kanade, is an ayakashi medium—an individual with immense vitality that attracts ayakashi. Matsuri deems all ayakashi threatening and wishes to keep Suzu as far from them as possible, but this clashes with her desire to remain close to them. One day, the pair encounters Shirogane, the "King of Ayakashi," who is hellbent on consuming Suzu. As she is about to be eaten, Matsuri comes to the rescue and manages to seal the ayakashi's powers—but not before Shirogane takes revenge by turning him into a girl! Until he finds a way to transform back, Matsuri must adjust to his new, peculiar lifestyle while fighting against hostile ayakashi. Moreover, Suzu is now conflicted about her feelings toward Matsuri—further plunging their relationship into a state of ambiguity.

On Christmas Eve, four-year-old Miri Unasaka arrives in Tokyo completely alone, in search of her father. The bright lights and merry atmosphere guide Miri to a big hotel and a man with a delicious-looking cake. However, the child has just unknowingly walked into the center of an elaborate, foolproof plan for assassinating a dangerous mafia boss. Professional assassins Kazuki Kurusu and Rei Suwa live together, fleeing memories of their grim childhoods and avoiding emotional connections. When their mission goes awry and they end up bringing Miri home, there is only one reasonable thing to do: return Miri to her mother. But the girl's innocent laugh and pure worldview quickly enamor her to Kazuki, who secretly enjoys playing a parent, and it is not long before Rei's impenetrable heart makes room for Miri. Miri's every move is unpredictable, and Kazuki and Rei find raising an energetic child harder than any of their missions. Although it presents a great risk to their careers, Kazuki and Rei—both assuming the affectionate nickname "papa"—decide to provide Miri with a normal childhood despite all the odds stacked against them.

Akio Honjou is a high school student with a special gift for music. He can perfectly recall any piece of music that he has heard only once. One day, as he tries to reproduce a particularly soothing piano melody, he unexpectedly meets Juri Makina—the girl whose cell phone had spontaneously played the tune earlier in class. If art is the only way to truly know what landscapes populate others' inner worlds, then can this particular tune pave the way for Akio to begin to understand the more intellectual and emotional aspects of his captivating classmate, Juri?

Earth has been conquered by the evil Illumidus Empire, with parallels drawn to the U.S. post World War II occupation of Japan. Captain Harlock with a group that will become his life long friends begin their fight against this tyranny visited upon the planet Earth, with no regard to the costs the struggle will have on them, caring only for the ideal of restoring freedom to the people of Earth.