超能力が科学によって解明された世界。能力開発を時間割り（カリキュラム）に組み込む巨大な学園都市。その街に住む高校生・上条当麻のもとに、純白のシスターが現れた。彼女は禁書目録（インデックス）と名乗り、魔術師に追われていると語る。こうして上条当麻は、科学と魔術の交差する世界へと足を踏み入れてゆく。

　摘要

　故事講述的是從東京都西部被分割出來的這座都市中，「超能力開發」被列為學校課程的一部分。在二百三十萬人口中，有八成都是學生，所以被稱為學園都市。他們每天都在超能力開發上進行相互競爭。根據能力不同，可以分為5級，從無能力到超能力。故事的主人公上條當麻是學園裡的一個無能力者，但並非完全沒有能力，而是他的能力是能夠將一切異能效果無效化。他只有右手能夠使用這種能力，還給自己的這種連上帝的奇蹟都能抹殺的能力取名為「幻想殺手」。而正因為他的右手似乎把神的祝福都給抹殺掉的緣故，導致自己一直過著不幸的生活。某一個暑假的日子，在家裡的陽台上，他遇見了一位修女，這位少女自稱自己的名字叫「禁書目錄」（Index），並是從魔術的世界逃了出來，現在正在被魔術師追趕中。就這樣，上條當麻一腳踏進了奇妙而美麗的世界，開始了上條當麻與御阪美琴的戰鬥……掌握了十萬三千本究極魔法書（魔導書）的少女與擁有抹殺一切奇蹟的上帝之手的少年，將面臨一系列故事……

　Ｐｌｏｔ

Toaru Majutsu no Index is set in Academy City, a technologically advanced Academic city located at western Tokyo which studies scientifically advanced superhuman students with powers, but is also set in a world where magic is real. Tōma Kamijō is a student in Academy City whose right hand, the Imagine Breaker, has the ability to negate any supernatural powers, but also his own luck. One day he finds a young girl hanging on his balcony railing named Index. She is a nun from Necessarius, a secret magic branch of the Church of England, and her mind has been implanted with the Index Librorum Prohibitorum—103,000 forbidden magical books the Church has removed from circulation. His encounter with her leads him to meet others from the secret world of science and magic and an adventure with his friends where science and magic collide. Tōma's unusual power places him at the center of conflicts relating magicians and science-based espers in Academy City. As Tōma tries to help and protect his friends, he learns the people he knows are not as they appear and begins to attract the attention of magicians and espers alike as they try to unravel the secrets of Academy City and Index.

The side-story, A Certain Scientific Railgun, focuses on Mikoto Misaka, an electromaster who is the third most powerful of the seven Level 5 espers in Academy City. Set before and during the events of the novels, the manga tells the adventures of Mikoto and her friends during that time period from their point of view.