A gigantic meteorite landed on earth a few years back. A mysterious capsule believed to have belonged to the aliens was discovered. Called the "black box," an international organization called "Project BB" was created to research it. Eight boys, including Manabu Yoshimura, attend International Academy, a school located near Project BB headquarters. They are enticed by their teacher Toukichi Hashiba's promise of "I'll give you class credit," and end up getting involved in his experiment. The experiment was to enter the eight empty chambers of meteorite. According to Hashiba's theory, the meteorite should strongly respond to strong human thoughts. He tells them to have a clear image of a great looking gigantic robot; if they do, something should happen... Then, a big spaceship appears in the sky and an alien calling himself Wercury appears in a 3-D image. He tells them he is from the Star of Prokimasi and that he has come to collect the meteorite of the Choshin people. If they do not hand it over, he will challenge the earth beings to a battle. Manabu and his friends are confused by the unexpected turn of events but the meteorite responds to the thoughts of the group and suddenly starts to transform itself into a gigantic robot. Then, attacked by the invading Prokimasi robot, they are forced to pull their strength together and fight back. But it is extremely difficult to put the wills of the eight together as one and the robot cannot fight in the way it should. The gigantic robot that Hashiba named "Gakusaver" and Manabu's eight; can they manage to protect Earth and the meteorite from the Prokimasi invasion?

The show starts with the tale of Chitose Fujinomiya, a girl who goes from riches to rags and back and remains a snob despite it all. When her wealthy father dies, remaining debts leave Chitose almost broke, and she is kicked out of the affluent Tokai no Gakuen, or City Academy. She is left with nothing in the world but the clothes on her back and one pink goldfish named Gyopi-chan, the only memento she has of her father. Wandering lost, she collapses on the grounds of the poor-but-happy Inaka no Chugakko (Country Jr. High School), where the students are rough if friendly, and farm animals regularly roam the school grounds and even attend class. Recovering, she enters into the school but is repelled by its air of poverty, to which she is unaccustomed.

On the front lines of the war, there is a little girl. Blond hair, blue eyes, and porcelain white skin, she commands her squad with lisping voice. Her name is Tanya Degurechaff. But in reality, she is one of Japan's most elite salarymen, reborn as a little girl after angering a mysterious being who calls himself God. This little girl, who prioritizes efficiency and her own career over anything else, will become the most dangerous being amongst the sorcerers of the imperial army.

Index is still a fugitive and many powerful Magical organizations and individuals want to take her to use the books in her memory eliminating her in the process. War between those organizations is also starting to emerge. Index can only rely on her friend Touma who has always protected her along with Misaka and other friends from the Academy.