Tokyo is flooded with countless heroes — chōjin — during the time of "apotheosis." Their origin stories are all different. While some were altered by evil organizations, others came from space, magical worlds, or are fairies from ancient times or robots. But the Japanese government could not simply close its eyes as these superheroes ran rampant.
In the year 2071, the Far East is ruled by angry gods. 20 years ago unknown life forms called “Oracle cells” begin their uncontrolled consumption of all life on Earth. Humanity both fears them and reveres them as "aragami." They are immune to all weapons and the mankind's numbers continue to dwindle. The last bastion of hope is the newly developed "God Arcs" weapons that utilize Oracle cells to fight back. The weapons wielders band together into an elite force dubbed "God Eaters."
Himari Takakura passes away after going out on a trip with her brothers, twins Kanba and Shōma. She was, however, miraculously saved by a spirit in a penguin-shaped hat. In return for her extended life, the twins must search for an item known as the Penguin Drum with the aid of three penguins, which are visible only to the siblings.
The incidents which occurred on August 14th and 15th bring a group of young boys and girls together… They are members of a group they call themselves the "Mekakushi Dan" (Blindfold Organization) and each member possesses a strange power involving their eyes.
Koyomi Araragi is a student who has recently survived a vampire attack, with the help of his friend Tsubasa Hanekawa. Now, he finds that she has been possessed by an oddity called the Curse Cat, and is now attacking people, including her parents. He must now find a way to help get rid of the Curse Cat.
During the month of October of his third year in high school, Koyomi Araragi is introduced to a transfer student named Ougi Oshino by his underclassman Kanbaru Suruga. Ougi tells Koyomi that she has something she wishes to consult with him. When she draws the map of Naoestu High School, she finds something peculiar. This discovery reveals a tale that wasn't meant to be told, and this makes Koyomi's high school life totally different. This is the story that brings to light “what” makes Koyomi Araragi. This is the story that reveals the “beginning” of everything.
After experiencing a bizarre dream, Madoka Kaname, a kind 14-year-old girl, encounters a magical creature named Kyube. Madoka and her friend Sayaka Miki are offered the opportunity of gaining magical powers if they agree to make a contract with the strange little being. He will also grant them one wish, but in exchange they shall risk their lives by accepting the responsibility of fighting witches. Invisible to human eyes, witches are catalysts of despair in the areas they inhabit. An ally of Kyube, a magical girl named Mami Tomoe, befriends and encourages the two girls to accept the contract. For an unknown reason, another magical girl named Homura Akemi is determined to prevent Madoka from accepting the deal.
Takeya Yuki is in love with the school. For her, it's a wonderful place, where she enjoys her school activities, especially the activities of her club: School Life Club. The club has Rii-chan as the president, Kurumi-chan as another member, and the teacher, Megu-nee, always there for them. Yes, she is in love with her school... in her mind. Because, for her, the reality of the school and their club's activities is way too hard to be perceived...
The story picks up immediately after the events of Grisaia no Meikyuu, with Kazami Yuuji having been detained for suspected involvement with an international terrorist organization, lead by Heath Oslo, that has managed to enter Japan's borders with a devastating new weapon of mass destruction in hand. Meanwhile, at Mihama Academy, the remaining students find themselves with time running out. Due to financial issues, the school is set to close within the month. Over the past year, though, the girls of Mihama have finally begun to find their own legs, thanks to Yuuji's involvement. Are they really just going to bury their heads in the sand and let the world change around them? And are they really willing to let the man who changed their lives slip away without so much as trying to win him back? As the end of their time at Mihama Academy approaches, Amane, Makina, Sachi, Yumiko, and Michiru find themselves arriving at a single conclusion.
How much a group of students can do in the face of countries and organizations far bigger than any individual could hope to be remains to be seen. In the first place, Yuuji's position is far more complicated than any of them could have imagined, as he finds himself embroiled in an elaborate game of super-political chess revolving around both himself and an inconceivable new system slumbering in the depths of CIRS—a system that Yuuji may have more of a connection to than he thinks. One thing is for certain, though—the girls of Mihama are no longer willing to let the world steal things away from them without at least a bit of resistance first. And with help from a mysterious individual known only as Thanatos, they may just achieve their goal...