There are 3 main organisations to choose from in MxO: Zion, Machines and the Merovingian. There are also 2 sub-organisations: EPN (from Zion) and the Cypherites (from the Machines). To be a part of a sub-organisation you need to be a member of the appropriate main organisation and join a faction with their tag. If you want your faction to have an EPN or CYPH tag contact the appropriate liaison officer on your server. There are other unjoinable orgs that come and go through the storyline. You show your loyalty to an org by gaining reputation from doing their missions and making a crew aligned to that org. The maximum number of crew members you can have in a crew is 12.
Zion
Leader: The Zion Council
Controller: Tyndall
Recruit: Redpills and Bluepills
Base: New Zion (Real world)
Playable: Yes
Zion is the last city of free humanity, located deep within the earth. It's called Zion because the Zion people consider it an idealized, harmonious community (a utopia). In the matrix, the Zion Organization stands for humanity’s right to determine its own destiny. Zion believes that a human being’s freedom to select his or her own destiny is sacred, and that each individual must be free to choose whether to live out their life in the comforting illusion of the matrix, or in the harsh truth of the real world. Redpills in the service of Zion are expected to risk everything for its ideals, and to be happy with a fair share of whatever prosperity may fall Zion’s way.
Machines
Leader: The Architect
Controller: Agent Gray
Recruit: Redpills, Bluepills and Programs
Base: Machine City (Real world)
Playable: Yes
The Machines are a race of self-replicating, sentient mechanical entities. They imprisoned humanity within the pods, and they power themselves with the bio-electric energies generated by a healthy human mind. They don’t want to destroy humanity, they are utterly dependent on humanity for their continued existence. The only thing about humanity that matters to the machines is that energy continues to flow out of the pods. They do not care if the humans are slaves or free unless their freedom starts to interfere with the energy fluxes. The Machines will make deals with human Redpills when it suits their purpose to do so. They are quite scrupulous about delivering whatever rewards they may have promised to the human operatives, but emotions like gratitude, generosity and mercy are completely alien to the machine mind. Although they are no longer engaged in active hostilities against Awakened humans, the Machines continue to guard themselves in the real world with the hunter-seeker units called Sentinels, while the cold and implacable AI constructs called Agents continue to oversee their interests in the matrix.
Merovingian
Leader: The Merovingian
Controller: Flood
Recruit: Redpills and Exiles
Base: The Chateau (The matrix)
Playable: Yes
When they built the matrix, the Machines found it necessary to create autonomous AI (Artificial Intelligence) constructs that would look and act like human beings. Inevitably, some of the AIs acquired free will, and then some of these free AIs began to comprehend the true nature of the matrix. These AIs, in turn, started to establish communication with other Machine AIs outside the matrix proper, and the matrix came to be known as a safe haven for these sentient programs who wished to flee the control of the Machine world. In The matrix an AI could feel, live and breathe as never before. A new life could be granted to those that wished to flee from the control of the machine world or avoid deletion. The matrix came to be known as a safe haven for these sentient programs. These 'Awakened' pseudo-humans call themselves 'Exiles'. The Merovingian (a name taken from an ancient line of kings in human history) is the most active and powerful of the Exiles. If he is not exactly the sole leader of the Exile community, he is certainly the first among equals, and he is by far the most active Exile player in matrix politics. He has spies and operatives everywhere in the matrix. He will cheerfully employ human Redpills whenever it suits him to do so, and he is quite generous in rewarding those who serve his interests.
Cypherites
Leader: Cryptos
Controller: Veil
Recruit: Redpills
Base: Unknown
Playable: No
The Cypherites are redpills who wish to be reinserted into the matrix. They are disillusioned with the real world and want to return to the simulated reality of the matrix. They also want to destroy Zion and reinsert all redpills so that nobody will ever be awakened to the horror of the truth again. They take their name from Cypher, the first redpill who wanted to be inserted back into the ignorant bliss of the matrix. Cryptos was friends with Cypher and he is determined to force the belief of his friend on every human, one way he does this is with cryptic messages he lectures from his boxes around the megacity. Cryptos wears a neclace with a bluepill pendant to show his beliefs. The Cypherites wear bandannas over their faces to mask their true identities, which is why they used to be called 'Masked men'.
E Pluribus Neo
Leader: The Kid
Controller: Shimada
Recruit: Redpills
Base: Old Zion (Real world)
Playable: No
Neo isn't around to lead humanity to freedom any more; he sacrificed himself to make the possibility of that freedom real. E Pluribus Neo (EPN) want to continue Neo's work. EPN (From many, One) are dedicated to following the way Neo opened for humanity and they are dedicated to freeing everyone from the clutches of the Matrix even if it risks breaking the truce. They aren't looking for excuses or truces, they are going out and doing what Neo died for and anyone who feels the same way can join them. EPN show their faith by the males dressing up as Neo and females as Trinity. They perform mass recruitment missions to get as many bluepills as possible to take the redpill and sometimes go to the extreme by planting code bombs to force bluepills to wake up in their pods in the real world. They are often in conflict with the Cypherites because their beliefs and goals are the exact opposite of EPN.