The concept of organizations within the Matrix refers to the various groups with an accumulated human redpill following which are vying for control or power within the Matrix or the Real.

Main OrganizationsEdit

There are three primary organizations which players can choose to join in the Matrix. These organizations are Zion, the Machines, and the Merovingian. All players begin the game aligned with Zion, but once they have completed the introductory missions, they may choose to join any of the three main organizations without any reputation debt to work off.


Zion is the organization most easily identified from the Matrix trilogy, and refers to the whole of the last city of Zion's government, military, and citizenry. Zion are the primary group involved with targeting potentials and awakening them from the Matrix. While this was sanctioned under the Truce brokered by Neo at the end of The Matrix Revolutions, the Truce was ambiguously "broken" in Chapter 8 of The Matrix Online, hurling Zion back into a war with the Machines and causing the Machines to quickly relabel all of their actions as "terroristic."

Zion, unwilling to bend to the will of the Machines, continues to fight for their freedom and the freedom of the bluepills they wish to awaken.

The city of Zion, for which the organization is named, was destroyed in Subchapter 8.3. Prior to its destruction, the majority of its inhabatants were safely transported to the fortified city of New Zion, around which the end of the Truce was centered.

Important Zion PersonnelEdit

  • Niobe, captain of the Logos II and field commander of Zion's operations within the Matrix.
  • Ghost, first mate of the Logos II.
  • Colt, captain of the Mjolnir II in Roland's stead.
  • Roland, Zion's commander in Lock's stead.
  • Lock, previous commander of Zion, civilian advisor after being discovered alive and transported to New Zion after having been presumed dead in the attack on Zion.
  • Tyndall, Zion's controller.
  • Morpheus, captain of the Nebuchadnezzar and later, the Nabonidus. Went rogue and was killed by the Assassin.

Other ZionitesEdit


The Machines' organization (whose operatives are commonly refered to as "Machinists") is one which has changed from time to time from the human perspective, but has remained relatively consistent from the perspective of the organization heads. Though the Machines have existed for well over a millenium, they only began recruiting redpill help following the establishment of Neo's Truce. In their heyday, the Machines offered operatives a chance to protect the Truce and the System, in effect also offering the ability to protect bluepills still connected to the Matrix. Under this directive, the Machines classified EPN and the Cypherites alike as threats, despite the fact that it was later revealed that the Cypherites were a Machine-inspired endeavor.

Following the end of the Truce, the Machines declared the entirety of Zion their enemies (whereas previously they had been treated as shaky allies) and have sought their destruction at every corner. Operatives are still given the opportunity to protect the System and those attatched to it, but with no Truce to protect, part of the allure has fallen off.

Operatives of the Machine organization receive the benefit of being exempted from Agent attacks that plague operatives of Zion, and may even be rewarded with a special black desert eagle handgun named the FM-1500 System Magnum, the standard issue weapon for agents of the System, if their service has been exemplary.

Important Machine PersonnelEdit

  • Agent Gray, controller for the Machinine organization.
  • Agent Pace, prototype human-machine liaison agent program.
  • Agent Griffin, commonly seen agent program which leads missions on occassion.
  • The Architect, creator of the Matrix and origin of any and all Machine directives within the Matrix.

Other MachinistsEdit


The Merovingian's organization is one which exists outside of the years-long conflicts between the Machines and the humans of Zion. The Merovingian exists to profiteer from the chaos caused by the war within (and in some cases outside) the Matrix. Whenever a new source of power emerges, the Merovingian seeks to acquire it for himself. Whenever one under his protection fails to pay his price, he sees that his payment is received. The Merovingian controls almost all of the exiles in the city through underhanded means, after having delivered most of them to the current iteration of the Matrix via the Trainman.

The Merovingian's employ is another organization which failed to recruit redpill operative prior to the Truce, likely due to ferocious warfare in the Real and the impending reset of the Matrix associated with the return of the One to the Source. However, when the Truce was brokered, the Merovingian sought to employ human operatives in addition to his regular host of exiles. Operatives of the Merovingian are offered considerable compensation at relatively little restriction. Power is a common motivation for joining the Merovingian, who currently possesses the widely sought-after Biological Interface Program.

Important Merovingian PersonnelEdit

  • The Merovingian, trafficker of information and head of the syndicate. Also refered to as "The Frenchman."
  • Persephone, jealous wife of the Merovingian, formerly a program involved in the caretaking of humans podborns.
  • Flood, controller for the Merovingian organization.
  • Malphas, the Merovingian's blood drinker lieutenant.
  • Ookami, the Merovingian's lupine lieutenant.
  • The Twins, ghost program assassins.
  • The Effectuator, controller of constructs and networks for the Merovingian.
  • The Trainman, program capable of transporting programs from previous instances of the Matrix to the current. The Trainman was killed protecting the General.
  • The General, exiled leader of the Machine sentinel force sent to destroy Zion before Neo's Truce. Currently the Merovingian's eyes and ears in the Real.
  • Beirn, last living Unlimit General coerced to the Merovingian's control through his lust for Persephone.


There are, at present, two sub-organizations which players can choose to join in the Matrix. These organizations are the Cypherites (the sub-organization for the Machines) and E Pluribus Neo (the suborganization for Zion). There currently exists no sub-organization for the Merovingian, nor do there appear to be any current plans to implement one. While there are no specific missions for either of these organizations, they do have their own live events and liaisons, and a player is generally recognized as a member of one of these sub-organizations either through communication and personal recognition by their server's liaisons (and through the servers, the developers) or by joining a faction established as Cypherite or EPN aligned (generally recognizable by the gold "EPN" or blue "CYPH" following a hyphen at the end of the faction name, though there are exceptions such as Recursion's "Daneiel Institute of Dream Interpretation" whose name was too long to fit in the code of the EPN tag).

Faction leaders can acquire a Cypherite or EPN tag for their faction by contacting their respective liaison and asking for it. Depending on the server, liaison, and circumstances, your request may be accepted or denied in any amount of time. On some occassions, factions will be asked to prove their alleigance. In the past, more or less complex riddles had been assigned to each of the sub-organizations for factions to solve in order to gain their appropriate sub-organization tag. However, there have also been several instances of factions receiving the requested tag with limited organizational involvement and little done to prove their alleigance.

Once the request is received and approved by a liaison, it is sent to customer service, who will apply the appropriate tag to the faction name. There is no specific time to this or any step of the process.


The Cypherites are a group who began as a loose confederation of Masked operatives who regret choosing the red pill and have traditionally aimed to return to a state of relative comfort within the Matrix. The Cypherites were initially led by Genmaskard and Enmaskarado, who made attacks on redpills shortly after the start of Neo's Truce. It was rumored that a former radical Zion operative named Cryptos was in charge of the Cypherites, and this came to light several months later when several boxes poppped up in the city filled with simulacra of Cryptos who spouted anti-redpill propoganda.

At their inception, Cypherites aimed to rid the Matrix and the Real of all operatives who attempted to awaken people from the Matrix before seeking to be reinserted into the Matrix. However, shortly after Seraph removed a program which had been controlling Cryptos and reporting to the Machines, Cryptos sought reinsertion and was told by Agent Gray that there was no such procedure. Most Cypherites now seek to protect the bluepills of the Matrix by stopping others from presenting them with the choice and by eliminating those who present the choice.

Important Cypherite PersonnelEdit

  • Cryptos, captain of the Blue Dreamer and leader of the Cypherites. Following Seraph's attack, also a mixture of program and man.
  • Veil, first mate of the Blue Dreamer and Cypherite controller. Also known as Toorima, previously a member of the Novalis II.

E Pluribus NeoEdit

E Pluribus Neo is a group formed by Michael "The Kid" Popper and Shimada in reaction to the activities of the Cypherites during the Truce. EPN operate more like a theocracy than Zion, placing great faith in Neo, many believing that he watches over or guides their actions. Most members of EPN place a great stock in the power of belief, which is exemplified by not only abilities within the Matrix, but even by Kid's own awakening through self-substantiation.

EPN members believed that Zion did not and does not have the proper goals in mind, and seek not only the return of Neo's body in the Real (as per Morpheus's wishes), but the destruction of the Machines, and that all humans plugged into the Matrix be offered the choice. EPN have, in the past, operated as a nomadic group in the Real, allowing them to make sporadic strikes against Machine targets, such as the power lines. Following the destruction of Zion and the migration to New Zion, EPN have cleaned up and fortified the old city and, while they maintain mobility and the capability to resume nomadic living, currently occupy the city. EPN are active participants in the war between Zion and the Machines on the side of Zion.

The phrase "E Pluribus Neo" translates literally into latin as "From Many, New," but is actually a take-off on the phrase "E Pluribus Unim" (From Many, One). EPN use the word "Neo" in refrence to the Zion operative and pseudo-messiah's handle and synonymous title "the one," making the sub-organizational title more akin to "From Many, The One."

Important E Pluribus Neo PersonnelEdit

  • Kid, captain of the Neo's Hope and leader of EPN.
  • Shimada, first mate of the Neo's hope and EPN controller.

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