The Disciples are a criminal organization, originally working under Overlord. Later on in the books, after Overlord is killed, Anastasia Furan takes over and makes the organization independant from the AI.
At the beginning of the book, a scene is shown where a disheveled Tobias Scheckter claims that the Disciples are after him to an officer that saw him in the middle of the desert. Soon after, Scheckter (and the officer) is blown to bits, presumably by the Disciples. Much later on, Jason Drake confers with them after being unable to capture or kill Dr Nero . The organization has been working with Drake, using him for his technology and placement as a former member of the G.L.O.V.E. ruling council. After Drake gets Darkdoom to cooperate with the plan by pinning the tradgedy about to happen on G.L.O.V.E., the Disciples tell him to kill the hostages (Shelby, Lucy, Laura, Franz, and Raven) except for the Darkdooms. This led directly to Raven escaping her holding cell and infiltrating the Dreadnought as it began to launch. In the end, it is revealed that the Disciples were using Drake, and Pietor Furan, a Disciple who had been providing manpower for the operation, kills him. Furan had also interwoven the supercomputer Animus into the Dreadnought ship on the order of the other Disciples, which is the second time we see how powerful it can be against Otto.