Cult of Science

The Cult of science (科学崇拝) is a mysterious organization who has indirectly poised as a minor antagonist in the novels and doesn't belong to either the magic side nor the science side of the Index universe and apparently is vent on investigating as much as possible about supernatural forces regardless of what side they belong to.

Background
The true scope of the Organization is not known, however Amai Ao as probably referring to them when he mentioned the existence of organizations that can escape from Academy City's influence. They have shown absolutely no true knowledge about either "Magic" or "ESP" nor even "Hard Science", due to their lack of knowledge they are sometimes treated with mockery by those who truly hold a grasp of the powers they pursue.

Deep Blood Arc

 * Main article:Deep Blood Arc

This is their first mention on the series, where it is revealed that they are the financing and administrative power behind the Misawa Cram School before Aureolus Izzard took over the building; they are also the ones responsible for the imprisonment of Himegami Aisa, who was initially captured roughly a month before the fight with the Alchemist.

Sisters Arc

 * Main article:Sisters Arc

When Misaka Mikoto broke into the institution that receives data from the Tree Diagram, she found in the installation traces of a report directed towards the "Science Worship", that detailed the current condition of the Orihime I

Three Stories Arc

 * Main article:Three Stories Arc

They offered shelter to Amai Ao when he planned to escape Academy City and create a large incident, this is -however- known to the reader much later.

Tree Diagram Remnant Arc

 * Main article:Railgun

Apparently they are also taking part in "the race" for retrieving remnants from the Tree Diagram, in fact it is possible that they are behind the information leak that has propelled several countries to launch space shuttles and search for remnants of the Orihime I. At the end of the arc Yomikawa Aiho leads Anti-Skill and pursues, defeats and captures all of the personal that was involved with using Musujime Awaki in order to get pieces of the satellite, it is here that it is also revealed that they had a hand in Amai's actions.