Sakura Kinomoto was an ordinary 4th grader until the day she opened a strange book and let dozens of powerful magic cards loose on the world. Keroberos, the Guardian of the Clow Cards, informs Sakura that it is now her responsibility to find and capture the freed cards. However, much to the reluctant Sakura's dismay, things aren't going to be easy for her. Simply saying magic words and waving her wand around isn't good enough. Each card is a living, thinking, extremely powerful being. She'll have to learn to cope with her new responsibilities, as well as ordinary troubles involving love, school, family, and friends. With the support of her friend Tomoyo and a young boy with powers of his own, she must learn how to use her newly awakened magical abilities to collect each card and prevent the disaster that will befall the world if she doesn't.
In the future, personal computers have developed into "Persocoms", mobile computers that look like human beings. Hideki Motosuwa, a prep school student, desperately wants to buy a Persocom but cannot afford to. One day he finds a Persocom that has been thrown away and decides to keep it. When he turns on the Persocom, all she can say is "Chii" so he decides to name her that. After a while it starts to become apparent that Chii is more than an average Persocom. Having much better performance, it seems that Chii might be a "Chobit", a type of advanced Persocom rumored to have independent thought.
Noriko Takaya's dream is to become a space pilot like her father, Admiral Yuzo Takaya. He died when she was still a little girl due to an attack of alien forces in deep space. After entering Okinawa Girls Space Pilot High School, Noriko is handpicked by instructor Kouichiro Ohta as someone with great potential. She must then persuade everyone, especially herself, that she can indeed fulfill her goal and become an accomplished pilot despite being just an ordinary girl.
Takeru continues his education at Tenbi Academy as part of the newly formed Security Committee. As a team with the other members they battle unscrupulous individuals who use their Maken for evil purposes. In the meantime, his libido and the conflicting romantic interests of the girls surrounding him complicate matters considerably.
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...
Kasuga Arata lived a normal life together with his childhood friend, Hijiri Kasuga, in a small town. However, everything changed on the day of the Black Sun, and a magus (mage) appeared before him. The Black Sun caused the Breakdown Phenomenon which destroyed the town where he lives. Because of this, his normal life was artificially reconstructed by a grimoire that his childhood friend had left. The appearance of the magus led him to a new life in the Royal Biblia Academy and meeting the members of the Trinity Seven.