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All lives besides my own are equally meaningless, except for Rena's. I'll revive Rena's conciousness no matter how many lives it takes.
~ Chisato Ichijuku
That is why I hate humans... They are illogical... and act based on emotions
~ Chisato Ichijuku

Chisato Ichijuku is a biochemist with a genius-level IQ working of The Organization on their experiments with alien parasites, which resulted in Mako Fujisaki and other "witches"- girls with superhuman abilities created by kidnapping young girls (it is not stated why only girls are chosen) and implanting them with an alien parasite. Chisato is a sociopath and a misanthrope, who places as little value on the lives of humans as he does those of insects, and expresses and outright hatred of humanity. For this reason, Chisato ordered the execution of all "witches" ranked "B" or lower, who he saw as useless, an event which in turn prompted the witches' escape and the other events of the series. The only exception his misanthropic attitude was his sister, Rena, who he loved dearly, and was devastated when she died of an illness. Chisato was determined to use, the alien biology to bring her back to life, and implanted an alien parasite in her body, which brought her back to life in the form of Kotori Takatori, a personality created and implanted within the parasite. Chisato intended to her sister's personality, which was still in her brain, take over the parasite, called a "Grane". The Grane would then hatch from Kotori, and destroy all life on earth on a cellular level. Then, Chisato believed, he and his sister would become gods of a new world.

Chisato used Mako Fujisaki as a pawn in his plan. Mako, for her part, willingly followed his orders as she had fallen in love with Chisato when he saved her life, rescuing her from an experiment involving a radiation chamber at great personal risk. Chisato, however, stated that he only rescued Mako as she was necessary for his plans. Mako follows his orders, even if he does not return her affection.

With Mako's help, Chisato puts his plan into action, kidnapping Kotori from her new home with protagonist Ryota Murakami and several other escaped witches. Murakami, along with Kuroha Neko, Kazumi Schlierzauer, and Hatsuna Wakabayashi. They are too late, however, and Kotori's "Grane" begins to hatch, and Ryouta is forced to kill Kotori on her own urging in order to save the world. With her last breath, Kotori reveals she was Rena all along, and tells Chisato that she never wanted him to cause all those deaths in order to save her, and makes him promise never to hurt anyone again, but rather to help those in need. After Kotori's death. Shortly afterwards, agents of Hexenjagd attack, having suppressed Mako's power's for only seven seconds. The agents open fire on Mako, but Chisato, taking his vow to work to save lives, jumps in front of the bullets, sacrificing himself to save her.

Mako is infuriated by Chisato's death, and decides to destroy the entire world as her revenge. Meanwhile, Murakami presses a button on Neko Kuroha's harness, which unleashes her hidden abilities (although at a high risk of death). Neko survives the process and engages Mako in combat, which ends in Neko using her new power of micro-black hole generation to swallow both Mako and the ball of antimatter she was creating, one large enough to destroy all of Japan.