In a world rife with deadly creatures called "youma", a young silver eyed woman, Clare, works on behalf of an organisation that trains female youma halfbreeds into warriors with the ability to destroy these creatures. Considered a rogue for picking up a stray child & almost losing herself to her youma side by "Awakening", she is constantly assigned rather dangerous missions...
Masamune Izumi is a light novel author in high school. His artist, known only as "Eromanga Sensei" is reliable but Masamune has never met him and assumes he's just a perverted otaku. Masamune's little sister is Sagiri, a shut-in girl who hasn't left her room for an entire year. She even forces her brother to make and bring her meals when she stomps the floor. Masamune wants his sister to leave her room, because the two of them are each other's only family.
One day Masamune discovers that Eromanga Sensei and Sagiri are one in the same. Further chaos erupts between the siblings when a beautiful, female, best-selling shōjo manga creator becomes their rival.
Naota is a normal Japanese 6th grade boy (although a little cynical), but when his older brother leaves for America to play baseball, his brother leaves his 17 year old girlfriend Mamimi behind. Mamimi is sending mixed signals and advances to Naota, and he doesn't know what to do about her. But to make matters worse, Naota's world is totally turned upside down when he is run over by a woman on a Vespa. During their first encounter, she hits him over the head with her guitar, which then causes a horn to grow out of his forehead. She calls herself "Haruko" and her presence changes Naota's life to even further insanity.
A gate appears in Tokyo's Ginza district sometime in the 21st century. From the gate pours out monsters, knights from middle-age Europe, and other fantasy-like beings, and they kill many of the citizens of Tokyo. This event is known as the Ginza Incident. The government sends a small group of soldiers from the Japanese Self-Defense Forces to the alternate world beyond the gate. Led by otaku soldier Yōji, they find that the villages in the world are being attacked by a dragon. An elf girl who is a survivor from the dragon's rampage joins the group in their travels across the dangerous new world.
Kraft Lawrence, a 25 year old peddler travelling from town to town selling and buying various things to make a living during a period much like Europe in the Middle Ages. One night when stopped at the town of Pasroe, he finds in his wagon a 250 year old pagan wolf deity girl named Holo. She appears to be that of a 15 year old girl, except for a wolf tail and ears. She introduces herself as the town's goddess of harvest who has kept it blessed with good harvests of wheat for many years. Despite having the responsibility to watch over the town, she wants to go back to her homeland in the north called Yoitsu, she believes the people have already forsaken her anyway and that she has kept her promise to maintain the good harvests. She manages to bargain her way out of the village by making a deal with Lawrence to take her with him. As they travel, her wisdom helps increase his profits, but at the same time, her true nature draws unwanted attention from the church.
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...