Mikoto Misaka, one of the strongest Level 5 espers in Academy City, gave her DNA map to a certain doctor when she was young, believing that it may be used for greater good. Unfortunately for her, it ended up being used to create countless clones of herself; forming the Misaka network, in order to create the strongest esper by sacrificing these clones whom she considers as her own sisters.
The Empire of Britannia has invaded Japan using giant robot weapons called Knightmare Frames. Japan is now referred to as Area 11, and its people the 11's. A Britannian who was living in Japan at the time, Lelouch, vowed to his Japanese friend Suzaku that he'd destroy Britannia. Years later, Lelouch is in high school, but regularly skips out of school to go play chess and gamble on himself. One day, he stumbles on terrorists 11's who've stolen a military secret and is caught by a member of the Britannian task force sent after them, who is Suzaku. As the rest of the squad arrives, Suzaku is shot for disobeying orders, while the military secret, a young girl, gives Lelouch the power of Geass, which makes anyone obey any order. While Suzaku is secretly made the pilot of Britannia's brand new prototype Knightmare, Lancelot, Lelouch becomes the masked Zero to lead the rebellion to destroy Britannia once and for all.
Ash is a student at Ansalivan Dragon Academy, attended by children who have formed contracts with dragons. He possesses the "star mark," the sign of a contract, but since his partner hasn't been born yet, he seems insignificant. The awakening of the dragon he's raising inside his body is triggered by an incident, and it emerges in the form of a young girl.
A freshman halberd named Harudori Tsugumi, befriends two other meisters, Tatane Meme and Anya Hepburn. All three take part in the NOT (Normally Overcome Target) class at DWMA (Death Meister & Weapon Academy ) and learn to control their powers in order to overcome their difficulties to have a normal life, as opposed to the battle-oriented EAT (Especially Advanced Talent) class taken by Maka, Soul, and their companions.
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.