Eleven years after the introduction of internet-connected, augmented reality eyeglasses and visors, Yoko Okonogi moves with her family to Daikoku City, the technological center of the emerging half-virtual world. Yoko joins her grandmother's "investigation agency" comprised of children equipped with virtual tools and powerful metatags. She quickly crosses paths with Yoko Amasawa, an expert hacker of the virtual environment, as Amasawa relentlessly seeks to "unlock" the mystery of a computer virus that emerges from an inaccessible corrupted space.
Narumi Fujishima is an ordinary high school boy who remains isolated from his fellow classmates. One afternoon fellow classmate Ayaka Shinozaki invites Narumi to join the gardening club and introduces him to a reclusive detective named Alice. Alice hires Narumi as an assistant and puts him to work solving the strange mysteries of Angel fix, an illegal drug. Little does he know it could put him and Ayaka in serious trouble.
Tokiha Mai and her sickly younger brother, Takumi, have received a scholarship to attend the prestigious Fuuka Academy. On the way, the ferry they are travelling on becomes the site of a destructive battle between two girls wielding apparently supernatural powers. This is only the beginning of their troubles, as Mai learns that she herself possesses these powers - the powers of a HiME.
Miss Kobayashi is your average office worker who lives a boring life, alone in her small apartment–until she saves the life of a female dragon in distress. The dragon, named Tohru, has the ability to magically transform into an adorable human girl (albeit with horns and a long tail), who will do anything to pay off her debt of gratitude, whether Miss Kobayashi likes it or not.
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...
At private Mihama Academy, five girls who seem normal attend the school due to "certain reasons." A sixth student "with reasons" named Yūji Kazami transfers in. Yūji has an ego with such darkness that he does not fade in comparison to the five girls, who are so different from the norm. As they each meet each other, they deepen their understanding of one another. Through the small bits of progress they make, each of their hearts will be affected. When Yūji arrives, a story of girls who are trapped by their pasts begins.