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Set in an alternate 19th century, the story focuses on an organization of exorcists, named the Black Order, as they defend humanity against the Noah Family, reincarnations of Noah and his twelve apostles whom bear hatred towards humanity and God led by a man known as the Millennium Earl. The exorcists' main weapon against the Noah Family are sentient holy artifacts called Innocence. Innocence comes in a variety of forms, varying from everyday objects such as boots to grandfather clocks, to weapons such as swords and guns; regardless of their form, each Innocence possesses unique offensive and supportive abilities and will only work for the wielder of their choosing. Out of the 109 Innocence hidden and scattered throughout the world, one of them is the master Innocence; whichever side obtains this Innocence first will win the war. In contrast to the Innocence, the Noah Family's weapons are derived from a power source known as Dark Matter. Dark Matter grants the Noah superpowers.

Academy City is a landlocked sovereign city-state whose territory consists of a walled enclave within Western Tokyo. It is the primary setting of the Toaru Majutsu no Index series and its side stories.
As the city's name suggests, it is a city of several schools and institutions of higher learning from kindergarten to university level that learn side-by-side along with the scientists who research on psychic powers and higher technology, the latter being one of the primary reasons for its establishment. It is the most advanced city in the world and its technology is said to be 20 or 30 years ahead of the world.

Academy City is composed of 23 districts, called School Districts which are simply numbered from one to twenty-three and each of these districts have a specific purpose.

In Mikado City (280,000 inhabitants), a "gate" to a different world suddenly opens one day. Monsters called "Neighbors" start appearing from the gate. Humans are overwhelmed at first when their weapons are found to be useless against Neighbors, until a mysterious organization appears that is able to repel the Neighbors' attacks. The organization is called the National Defense Agency, or "Border", and has appropriated the Neighbor technology called "Triggers", which allows the user to channel an internal energy called Trion and use it as a weapon or for other purposes. By activating a trigger, the body of users is replaced by a battle-body made of Trion which is stronger and more resistant.