At the beginning of the series, The Syndicate is introduced as a mysterious underground organization with no apparent objective. Its operatives work with both Contractors and Dolls to achieve their objectives, and even have access to ME technology in order to erase sightings of their affairs from witness' minds. The Syndicate makes extensive use of "word of mouth" communication in relaying both missions and operative status. In the face of it, it seemed that MI-6, the Japanese police and most crime fighting organizations were hunting down the Syndicate.

However during the course of the series, it is revealed that The Syndicate is in fact merely another facade for a global organization, in control of the PANDORA institute, that declares to be looking for stabilizing the planet's status and destroying the Hell's Gate. They had known allegiances with MI-6 and the Japanese Police Force. The current status of the organization is unknown. At the ending of season 2, a new Syndicate is formed consisting of Miskaki Kirihara, Goro Kobayashi, Oreille and Mao.

At the end of the fourth episode of The Black Contractor Gaiden, it was revealed that the Syndicate had been originally formed to prevent the prophecies of the Mitaka Documents from coming true. This was 50 years before. Since then, many organisations had fought among themselves, wanting the Syndicate's great power, and because of this, the Syndicate lost sight of its original goal. Towards the end of the episode, Goro Kobayashi looks at the body of Yin, sealed away in a cryogenics chamber, and comments to Yoko Sawasaki that they had been on the wrong path for a long time.