The Machinists arose after the Truce was established between Neo and the Machines. These awakened human operatives believe that peace lies in working together with the Machines instead of against them. As a result, they often clashed with their Zion counterparts in favor of the Machines.
Agent Gray was assigned as their controller and often met with them to discuss matters and answer questions that may have. He was often paired with Agent Skinner until the program's untimely demise at the hands of the Assassin. Eventually Skinner was replaced by Agent Pace , the first known female agent program.
After the Truce ended due to the discovery of New Zion, machinists found themselves in turmoil with themselves. Many were unable to comply with the Machines' orders. Some even left the organization to avoid engaging in hostilities with Zion in the real world. Others were more than happy to accept the Machines' requests. At this point the lines between Machinist and Cypherite began to blur and the two organizations were seen as no different from one another (aside from the Cypherites having much more extreme methods).
In the end, the Machinists contributely greatly to the battle against the Oligarchs and the salvation of the Matrix.
- The Apostles
- Special Investigation Unit
- The Undisclosed
Controller: Agent Gray
- BlazinWolf (trigger-happy operative)
- Rebirth Of Eden
- Systematic Chaos
- Project Mayhem
- The Tetragrammaton
- The Glitch Society
- The Watchmen
- The Imperial Order
- The Collective
- Mega City Department of Energy
- The Rakshas
- LEG10N (later went Cypherite)
- Guardians of the 7th Gate