Dark Side of Academy City

The Dark Side of Academy City (学園都市の抱える闇) refers to the criminal underworld of Academy City. Reaching to the very top of the city's administration, as stated, it is often engaged in criminal enterprises, such as human experimentation, espionage, and assassinations. Much of the science side story lines is concerned with the characters struggle against the Dark Side of Academy City. Indeed, an entire story cycle is dedicated to this premise. The name refers to the contrasting image of what the Academy City wants to portray, a technologically advanced city filled with students wanting to become espers.

After the events of World War III, though many factions from the dark side have been forced to disband, this part of Academy City still exists.

Origins and evolution
The origins of the Dark Side of Academy City apparently evolved out of the need for the higher-ups of the city to have more security to protect the city's assets like the various research institutions. Officially, it is Anti-Skill that guards the security of the city, however, due to the powers of espers, as well as the developed military technology of the city, the organization's structure and equipment with dealing with them has been weakened. This "Darkness" fills the role of security where Anti-Skill cannot provide. People from the Darkness provide protection and security to important people and the various research institutions. This is born from the members of the Board of Directors and other important persons hiring personal bodyguards as well as companies and research facilities hiring private armies. The Darkness hired are composed by a variety of people, from individuals with esper powers and special abilities, to failed students or persons who are selected for a specific purpose. An example of the latter would be Accelerator, who is "recruited" under duress by the GROUP liaison to work for GROUP. Though each organization and the personnel in them has their own quirks and skills, somehow or another each of them has a dark past behind them. The form of the Darkness as seen in the current year of the timeline has several factions working for the city against one another such as GROUP and MEMBER, as well as factions opposed to the city itself like Skill-Out and BLOCK.

Apparently, factions from the Darkness such as ITEM are all known to Aleister Crowley, and can be controlled by him.

Culture
Much if not all operations done within the dark side of Academy City is done in secret. This attribute has likely contributed to the unique subculture of the dark side of Academy City. An example of this unique culture is that those who have been sold into an organization can be hunted down by others if they attempt escape, as with the case with Nunotaba Shinobu. Another is when Tsuchimikado Motoharu's apparent "execution", where it is revealed that when agents of the dark side are convinced that someone is executed and dead, they will not go after that person again because they have convinced themselves as it is an etiquette of the dark side.

Espers are either used for experimental purposes or are recruited to the dark side of Academy City. Notable examples of this are Accelerator and Kinuhata Saiai, both were used for experiments in their younger days and later become operatives in the "Darkness" using their powers to aid their organizations. As the Board of Directors are involved, both Judgment and Anti-Skill are often powerless when it comes to dealing with the forces of the dark side, often with the higher-ups meddling through sheer bureaucracy and red-tape or the withholding of vital information. An example of this is when Anti-Skill is unable to enter Dangai University's Database Center during Skill-Out's attack of it. A triumphant example of this is STUDY, using their company to fund their operations.

Money is still a powerful motivator for organizations however. Factions such as ITEM and Scavenger are paid for the missions they successfully complete. However, organizations that are in the "Darkness" out of principle such as Disciplinary Action, in their quest for justice in the city, and Komaba Ritoku's Skill-Out, gathering armed Level 0s to oppose abusive espers, can be found.

Organization
What seems to be the difference between petty gangs like the ones led by Okahara Ryouta, Elder Sister, or the ones that Misaka Mikoto deals with and the factions in the "Darkness" is that they are far organized than them or at least have some connections with powerful people in Academy City. Indeed, even Skill-Out factions such as that of Komabata Ritoku's organized enough to become a threat to Academy City, had caches of money for their operations, and after the death of Ritoku, was tasked by Academy City itself for the assassination of Misaka Misuzu. Even though in many cases, the Skill-Out "Darkness" are not fully informed of the work they do. Regardless, Skill-Out is used from things such as temporary staffing to things that are illegal like human trafficking. Even Big Spider had connections with the outside allowing them to procure weapons, as well as in the inside that allowed them to use Capacity Down from Therestina Kihara Lifeline.

As for the factions that work for Academy City, they are usually composed of field operatives, a mediator, and a large support staff. The most well-known setup for this is that there are four field operatives that answer to a mediator or a liaison with the higher-ups and a large staff that supports them during missions. Mediators or liaisons are often shown as mysterious men on the phone, acting as an in-between for the higher-ups, maintaining the confidential nature of their operations. An exception of this is MEMBER's Kouzaku Mitori, who also acted as a field operative and made contacted the members in-person. After the revelation that she worked for Kihara Gensei in order to use MEMBER for his own gains, MEMBER begins operating on its own without a liaison.

As for the support staff or subordinate organization, that do things from menial labor such as transporting prisoners, corpses (including members of the field operatives), to complex background work such as the technical department which supports the organization by giving the members useful technical aid.

A unique faction within the "Darkness" is the Hound Dog, which is controlled by Aleister Crowley, and is a more like a military unit.

Prior to the events of World War III, if GROUP is anything to go by, it is implied that there is no way out of the organization other than dying. Motoharu says to Accelerator that if he followed the rules laid out by the Board of Directors then they will not let him out. He says that the organization is made so they profit no matter what happens. Still, it is likely incarceration can allow people to escape the "Darkness", however, people can still recruited even there, this is exemplified by Kouzaku Mitori being used by Kihara Gensei. Indeed, there are rumors that students from the Reformatory will suddenly disappear for reasons unknown, specifically high level espers or excellent students. When the guards report it, they are waved off and ignored. It is believed that Academy City makes some deal with the students and then release them in secret, and it may be more convenient to pass some of the missing off as dead.