The Matrix Online

The Matrix Online (also known as MxO) was a massive multiplayer online role playing game developed by Monolith Productions. It was the official continuation of the storyline of the Matrix film series. The game began closed beta-testing in June 2004 which was opened for people who pre-ordered the game before or during November 2004.
Warner Bros. and Sega officially released MxO on March 22, 2005. The game ran continuously from then until it was shut down on July 31, 2009 at midnight. The player assumes the role of a Redpill. When creating a new character, the player is given the choice of taking the blue pill (quit the game) or the red pill (continue the game). After the tutorial, the player is free to roam around the Mega City.
==Combat==
Combat is divided into two separate parts: Free-fire and Interlock. Free-fire mode allowed for large gun battles to take place, while Interlock is often broken down into bullet-time-affected martial arts moves. There were three main classes in the Matrix Online: Coder, Hacker, and Operative. Coders create special simulacrum that fight for them. Hackers manipulate the code of the matrix to affect friends or enemies from a distance, either damaging them, downgrading their combat abilities, or healing them and upgrading their powers.
Operatives are the soldiers seen from the movies- Martial Artists, Gunmen, and the spy class, which revolves around stealth fighting and knife throwing. When taking or dealing damage, the players damage influences are pitted against the other players resistance influences of the same damage type. Higher resistance versus lower damage means that the defending player will not take as much damage. when attacking or defending against attacks, one players accuracy influences are pitted against another's defense influences of the same attack type. 
==Organizations==
After the initial set of introductory missions, players can join one of the three main organizations working within the matrix each with a different set of goals, beliefs and methods: Zion, The machines, and the Merovingian.
====Zion:====
Zion is the last human city on earth, hidden deep underground and is chiefly concerned with protecting its citizens from the machines who see those who have awakened as a threat to those still connected to the matrix. Those who choose to work for Zion usually enlist in the Zion military and see this as the best way to protect their ideals of freedom.
====Machines:====
The main motivation for choosing to side with the machines is that this organization is seen as the most conducive towards maintaining the status-quo of the matrix and protecting the lives of those still connected to it. However there are those who feel that the only way to improve relations between man and machine is to work with them as closely as possible and see joining this organization as the best way to do so.
====Merovingian:====
Those who work for the Merovingian are in a unique position in that they need not concern themselves with the traditional hostilities between Zion and the Machines, preferring instead to act only when the situation would prove advantageous for themselves or the organization as a whole. However, this organization has also been chosen by some players as it is the only one out of the three organizations that fights to protect Exiles who reside within the matrix.
====Sub-Organizations:====
*EPN-E Pluribus Neo (Zion Aligned)
Members of EPN are devoted to what they deem "Neo's legacy". This mostly involves giving all human beings the opportunity to question the true nature of their reality, the matrix and to have the choice of the redpill or bluepill. Very much against the machines, and Cypherites in particular, there are some more fundamentalist schools of thought within this organization who believe that the only solution to humanity's problems is to free the entire human population from the matrix. They are led by The Kid with his old friend Shimda-who also acts as their mission controller.
*Cypherites (Machines Aligned)
Usually seen as the more extreme element of the machine organization, Cypherites follow in the footsteps of Cypher, wanting to be reinserted into the matrix as bluepills so that they may be blissfully unaware of the true nature of the matrix as a computer program. The name of their hovercraft, The Blue Dreamer, reflects this philosophy. They are led by Cryptos and his second in-command, the Zion-traitor, Veil. 
===Servers (Monolith Pre-Merge)===
*Linenoise
*Proxy
*Output
*Regression
*Heuristic
*Input
*Enumerator
*Iterator
*Method
===Servers (Post-Merge)===
*Vector was a Hostile server. Unlike the other servers where PVP is optional, players are flagged for fighting after they reach level 16. Vector was composed of players from the Enumerator, Heuristic, and Input servers.
*Syntax was a non-hostile server. Syntax was composed of players based from the Linenoise, Proxy, and Output servers. It was the Unofficial RP Server. 
*Recursion was a non-hostile server. Recursion was composed of players based from the Method, Regression, and Iterator servers.
==Story and Events==
===Race to find the One===
The first major event to occur in The Matrix Online was a "race" between the three organizations to gather Neo's RSI fragments. The organization that collected the most in a week received a defense bonus. Different organizations won on different servers.
Shapers were found that could manipulate the RSI fragments into the shape of Neo's mental projection. Unfortunately some Shapers were captured by a fourth party (The General). Those Shapers were forced to create super-Agents which the organizations worked together to defeat. Morpheus has also complained that the physical remains of Neo were never returned to Zion from the Machine City (Zero One), yet cryptically, the Machines have said that they did not recycle Neo's remains either.
===Red-eyed Agents===
The second major event a week later was the appearance of Agents with glowing red eyes. These Agents appeared mysteriously and began attacking all humans, including those allied with the Machines. None of the three factions claimed to be controlling the Red-eyed Agents, and some believe they serve a new fourth organization. They attacked anyone with an RSI code fragment ("contraband fragments") or anyone attempting to defend them.
Later, a message from the Oracle indicated that "intruders" angered by the Truce are behind this, and that somehow Neo split himself up into fragments within the Matrix knowing that it was needed for the future. However, the only way to put Neo's code back together is with the help of programs known as Shapers. Fighting then broke out between the factions for control of Shapers, leading to the Red Eyed Agents capturing a Shaper in the confusion, which allowed them to create a new breed of red eyed agents: "N30 Ag3nts". Soon Niobe sent a message to players to fight the menace along with a new wave of agents which bore a strong resemblance to Neo.
===Nightfall===
The third major event began with the kidnapping of two important leaders from vampire-like and werewolf-like Exile gangs (the Blood-drinkers and the Lupines, respectively). It was soon revealed that Malphas and his Lupine counterpart Ookami had not been kidnapped at all, but were hiding from the Merovingian. Upon returning, they led a revolt of both gangs against the Merovingian's domination of all Exiles, attempting to rally many humans to their cause. However, while Malphas was absent his subordinate, Invalesco, attempted an underhanded power grab against him, promising to turn humans that joined him into immortal 'vampires' with his source code. He was unsuccessful: upon Malphas's return, Invalesco was hunted down and killed. Amidst this infighting, the Merovingian was able to defeat the uprising and capture Malphas and Ookami. Subjected to torture in the Frenchman's Chateau, they were (for now at least) bent back to his service out of fear, and the attacks ended.
===Hunt for Morpheus===
Morpheus stepped up his quest to convince the Machines to return Neo's body. By planting specially coded bombs near places where redpill players were likely to gather (usually hardlines, but later on or near monuments), the bombs would detonate and, while they did no physical damage to the Matrix, spread a virus to any redpills caught in the blast. This virus was designed to reveal the underlying code, showing the bluepills the true nature of the Matrix, causing them to reject it as real, and possibly crashing the system.
All organizations were out to kill him. Agents patrolled the streets, as did the Lupines and Blood Drinkers. Another mysterious group emerged during this time, called Cypherites by many players, consisting of masked humans. Not only did they sabotage hardlines to trap people in the Matrix, but they also rabidly hunted Morpheus. Players rushed to defuse Morpheus' bombs in order to protect the truce, while others fought to protect the bombs.
On the sixth day of the ten day event, tragedy struck. Morpheus met a mysterious assassin as he set one of his final bombs in a waste water treatment plant. He fled the initial attack, only to be caught off guard when the Assassin caught up to him, apparently able to bend the rules of the Matrix as he slipped through a narrow vent in front of him. He was unable to dodge the onslaught of gunshots. Morpheus was dead.
Niobe met with leaders from the machines, who denied involvement. She later formed a faction of her own to track down who had sent the Assassin. The hunt for Morpheus' Assassin was on. Soon, exiles called Corrupted began to appear throughout the Matrix, attacking players at random. It was later discovered that these programs were created by the Assassin in his own image using a "corrupted virus", meaning that the programs' bodies were composed of flies, just like his.
During the chaos that ensued with the attacks, Agent Skinner, liaison to the Machinist redpills, was permanently deleted by the Assassin. Soon, players found documents on the Corrupted that were attacking them, and piecing the information together from it they learned that killing Morpheus had not been the Assassin's ultimate goal. The Corrupted were designed to destabilize the Matrix upon death, and by releasing them en masse, the Assassin hoped that players killing them would completely destroy the Matrix.
The event culminated with much larger versions of the Corrupted, called Complete Corrupted, who could only be destroyed by special pesticide items. All players of all organizations put aside their differences and worked together to defeat these massive programs and restore order to the Matrix. However, with the event over and order restored, one thing remained: the Assassin was still at large.
Following the permanent deletion of Agent Skinner, the Machines activated a new Agent as his replacement, Agent Pace. Agent Pace was a 'new style' of Agent, most notably in two ways. First, it was more emotionally expressive. Second, "it" is a "she"; Agent Pace is the first 'female' Agent. Pace's behavior is markedly different from previous models of Agents because she was designed to be "more human". Pace actually smiled on occasion, and behaved almost benevolently toward human redpills under her authority. "Pace" is Latin for "with peace", commonly taken to mean that no offense is intended by the speaker.
===Choice and Consequence===
The crew of the hovercraft Novalis II must try to save the life of their crewmate, Neurophyte. This scenario had alternate endings which played out differently on the separate game servers. However, with the later merger of the 9 servers into 3, plot continuity errors occurred. Walrus, an administrator for The Matrix Online, has stated that this storyline has been dropped instead of fixing the plot conflict.
===Double Cross===
The Cypherites, masked redpills that want to be put back into the Matrix like Cypher once did, begin a string of attacks led by Gemaskeerd and Enmascarado. In the end Enmascarado is killed by the Assassin, releasing a flame virus attached to his body, and Novalis II crewmember Toorima is revealed as a Cypherite leader called Veil , but not before she is able to kill her crewmate Vashuo.
===Death of the Destroyer===
Eventually, the Redpill forces create a weapon that can kill the bug-based Assassin - Insecticide. Realizing his imminent doom is quickly approaching, the Assassin split himself into multiple, weakened copies, which all spread out across the Megacity to do as much damage as possible, in the hopes of destroying the Matrix before he was deleted. As battle raged across the city, the Redpills managed to destroy all but one copy of the Assassin, of whom Niobe and an unnamed operative chased down and destroyed. In the aftermath, Niobe creates her own splinter faction dedicated to the deletion of the Merovingian, who had allegedly hired the Assassin originally.
===The Enigma of Cryptos===
The Sentinel newspaper says that soon, boxes will appear around the Megacity as part of an "amazement" by a bluepill street magician, Cryptos. A Zion hidden message is in the same Sentinel, and says that Cryptos was the name of a Zion operative who disappeared not long ago. 
Shortly afterward, boxes appear around the MegaCity as the newspaper said, which opened every two hours with Cryptos inside, who then gives a speech that sounds like it could be Cypherite propaganda, though he never mentions things very specifically. Operatives are sent on missions, and find some clues connecting the Cypherites with Cryptos.
===Veil of Cryptos===
Veil is broken out of the Zion prison, and as it turns out, she is the Cypherite mission controller. It is also discovered that Cryptos is the Cypherites' leader. The Merovingian makes something of a truce with the Cypherites, but worked against them as it suited his purposes. The Cypherites eventually discovered this, and their truce was broken. 
Meanwhile, Zion's main agenda is taking down the Merovingian, and the General's men create more powerful versions of the holy water, silver bullet, and wooden stake killcode items for killing exiles.
Meanwhile, The Kid founds a splinter group of Zionites, "E Pluribus Neo" (with his controller, Shimada). This organization is deeply loyal to Neo's vision of freeing humanity and violently opposed to the Cypherites.
===A Piece of Blue Sky===
Major Event that took place during May 09 through to May 16 2006.
Operatives are directed to report any unusual occurrences to their commanding officer (liaison) immediately. 
There has been much activity in the Matrix leading up to the Anniversary Event, and anticipation is growing amongst redpills across the world. It is rumored that there are disruptions in the Code; Veil and Shimida have been known to discuss the issue to Redpills on the Recursion and Syntax Instances of the Matrix.
Also, it has been introduced that there are splinter organizations within the Cypherites and E Pluribus Neo who are willing to go to even further extremes to achieve their goals. While much is going on among all organizations, Niobe and the General are formulating an attack on the Merovingian.
With the appearance of the extremist Cypherites known as "Sleepwalkers" attacking unsuspecting redpills in every alley, the activity within the Matrix increases, with many believing the newly sprung concert sites are linked to the Sleepwalkers somehow.
On the final day of the event, the concert began, and many redpills do indeed have their worst fears realized. A message blasts out from the speakers, threatening all redpills around and telling them to prepare for reinsertion. Moments later the Sleepwalkers appear en masse to attack the redpills gathered in the parks, or rather to distract them, as the huge concert lights blast out an eerie blue light, destabilizing the Matrix around them. Security officers of a redpill nature appear to fight off the redpills at the lights and re-activate them at every opportunity they get.
However, no matter how dire the situation became, the redpills managed to defeat the Sleepwalkers and re-route the power of the lights back into the Sleepwalker forces, re-inserting their bodies but leaving the rest of the redpills unharmed.
With the enemies defeated, organizational leaders appeared to congratulate their operatives, and the parties began.
===Grabbing the General's Stolen Items===
Now that a firm alliance between Zion and the Commandos is placed between them, the General offers Zion two items that he stole from the Machines (with Zion being unaware of it at the time) under the guise of "cheat codes." Anome, a Zion operative working under Niobe's command, swats out a key as the General throws it to Niobe. In critical missions, the Zion operatives work on recovering the key, while the Machines try to recover it, and Merovingian operatives attempt to gain it for themselves. On the Vector instance, Zion manages to grab the package from the messenger. Shortly after recovering the key, the Zion operatives give the key to Niobe. The Machine operatives commence a "First Strike" operation against the General by capturing the heliport in Morrell.
===Saving Captain Niobe===
Niobe tests out the chemical vials in the package while inside the Bishop Imports building, only to be betrayed by Anome. Every Zion operative that attended this particular meeting are killed in the resulting gunfight. Niobe is trapped on the 29th floor, and all means of reaching her floor have vanished due to a firewall created by the vials. With Ghost playing the role of negotiator, Zion is forced to create a temporary alliance with the Merovingian in order to trace Niobe.
Machine operatives do a damage assessment investigation on the effects of the chemicals ingested by Anome's operatives. On the Recursion instance, the efforts given from the critical missions helped Ghost lead a successful rescue operation of Niobe. On the Vector Instance, the General makes a permanent disappearance from the Matrix shortly after Machine operatives catch up to him, hinting at a vague return in the future.
===Anome's Unlimit===
After Anome and his men retrieve the case of cheat codes, they drink them and gain super powers and green-glowing, code-dripping eyes. Anome's men, having no limits to their powers, are named the UNLIMIT by Anome. Anome is no longer considered an operative and is labeled by Zion and the Machines as a rogue and a terrorist. They, the Unlimit soldiers, then focused on killing Bluepills by means of taking down the company Pendhurst-Amaranth (P-A), who supply Bluepills with Tastee-Wheat, and manage their water supply. Thanks to numerous missions by Redpills of all organizations, most attempts have failed, though the Zion correspondent from P-A, Brenda Utley, has gone missing. Attempts are being made to track her down and rescue her before Unlimit kill her. This is accompanied by increased Unlimit activity in all areas of the Matrix.
Brenda Utley was then rescued by EPN operatives on the Syntax Instance, with the last critical mission on this chapter stating that she found out about an Unlimit mole within the Board of directors. Zion operatives follow up on the lead, trying to eliminate the mole.
On the Machines' perspective, they were given a lead by an Unlimit operative named Meillak who had information on Anome's whereabouts. However, Anome caught on and had his loyal operatives attack Meillak. The machine operatives eventually decrypt the clues from various sources on Anome's whereabouts.
On the Merovingian's side of things, the Merovingian attempted to synthesize the cheat codes extracted from Beirn, an Unlimit officer who had an obsession with Persephone, but the attempts had failed as Machine operatives had destroyed the manufacturing equipment. As a result of testing the code, the Merovingian was able to detect fragments of the Twins' RSI, with operatives being sent to recover them. At the end of this chapter, the Twins were back and fully functional.
===Morpheus' Return?===
An operative reported a private message he received from someone claiming to be Morpheus: 'I am Morpheus... Captain of Zion...Urgent message for all Zionites...Neo...Not dead...Machine City...hurt...Machines...Return Neo...'. The message was soon relayed to others. Some either believed it wholeheartedly or attempted to reveal it as a fake. Following up on the rumors came the report that Seraph had been frantically searching Moriah Projects for someone.
This was followed soon afterwards by EPN and Cypherite operatives investigating the claims, searching the area that the operative had reported getting the message. EPN forces began to use 'Code Pulse Devices' around the city; devices that, although similar to the code bombs that had been used previously by Morpheus, are harmless to bluepills, and are simply a way to extract sensitive information from the Matrix.
Despite interference from Cypherite and Machine forces, EPN had discovered something vitally important. Over the past 8 months, at three different points in the city, at three different times, a signal had been appearing in the Matrix. Not matching any known code configuration, the signal did, however, have a signal associated with it, that of a Zion hovercraft Captains' beacon signal, although it was unknown which one it belonged to. Collaborating with Ghost and Zion Control, Shimada and EPN operatives discovered that the signal belonged to the Nabonidus' Captains' Beacon; Morpheus, the captain.
EPN's leader, The Kid, contacted Niobe and requested a meeting in Moriah Projects. Surrounded by Zionites and EPN followers, The Kid attempted to show Niobe his belief in Morpheus' still being alive by placing a Code Pulse Device at his feet; supposedly during a time when he believed the signal would appear again. For an hour, Niobe, afraid that she and the Zionite forces being near the Device would pose a threat to the Truce, attempted to persuade The Kid to disable the device. Her fears growing, Niobe eventually tried to disable the device herself, but instead was unable to go near the device due to a suppression field being placed by the crew of the 'Neo's Hope', The Kid's hovercraft.
Upon detonation, a shimmering RSI appeared. Some claimed the outline was very similar to Morpheus, and the same witnesses all agreed that the RSI was severely injured. The Kid suddenly vanished, leaving Niobe, the Zionites and EPN followers to flee from the quick retaliation of the Agents.
Meanwhile, the Merovingian noticed that profits had been dropping severely in the neighborhoods of Richland. Investigating a known trouble-maker Exile leader by the name of Silver led operatives to his rival in business, an inventor by the name of Mercury. Mercury denied holding back profits and stated that another enemy of his, Thallia, had been disrupting his business. The Merovingian ordered the Twins to interrogate her, which yielded information on where Mercury's workers were taking their business affairs, to his former lover, a promiscuous Exile by name of Raini.
The oblivious Raini revealed that Thallia and Mercury were actually working together. Malphas led a force to divulge information out of an Exile leader working for Thallia, who told the Merovingian that they had been hired by Anti M. After torturing Mercury and Thallia, and blackmailing Anti M's lover, Beryl, the Twins found her, where they learned that she had been hired by none other than the General, who had mysteriously vanished months ago.
As for reasons behind the General hiring Anti M, it is highly probable that it was to help facilitate observations on Sati, as hinted in the 6.1 Cinematic.
===The General's Attack===
While Zion and the Machines were busy with negotiations, and the Merovingian were busy getting business back in order, a strike force of Commandos kidnap Sati. Seraph jumps aboard a Black Hawk helicopter to fight her captors, only to be knocked off the helicopter falling into the Aquaduct. Meanwhile, shortly after recovering the vials, the Agents that killed Anome dropped the vials into the river, the reason for which is not known.
Zion has ordered operatives to protect the Oracle while fighting off regular and Elite Commandos (Commandos in a sneaking suit with single-lensed thermal goggles), as well as periodical Merovingian attacks. The Oracle gives Zion operatives cryptic hints on how to deal with the General, that they would have to find a way to bait him out of hiding.
The Machines investigate into the kidnapping to find out that the helicopter was unmanned, but operated by remote control. As a result, EPN operatives on the Syntax instance attempt to disrupt two other helipads with code pulse devices in order to reduce the number of operable helicopters, which was a success. The Machines also manufactured a virus in order to track down the locations of the General, and learned of a commando base in the real world, code named "Stalingrad".
Taking advantage of the chaos, the Merovingian attempts to extort the Oracle, but fails. Frustrated by the Oracle's refusal, he turns to numerous Exile contacts to get access to the kill-codes for the Oracle's current shell, but none of the contacts had the means nor interest to aid the Merovingian. As an act of desperation, the Merovingian turns to the General and requests for an alliance. As a result, the General accepts the Merovingian's request.
===The Return of Seraph===
The 7.1 Cinematic revealed a wet return from the river for Seraph. Emerging from the Bathary Row access node, Seraph approached three redpills and attacked one, MoonAvatar, without provocation. As MoonAvatar fell to the ground, Seraph performed what could only be described as a 'code exorcism', placing his foot on the neck, his hands over the body and extracting some unknown code from the victim.
So began Seraph's spree of attacks across the Megacity, both Red and Bluepill, without a word to anyone. Each victim would recover eventually, and would not remember the past few months. Although Seraph his attacks seemed random, after a few days a group of redpills managed to approach him and asked him for his reasons behind the attacks. Seraph, who now sported a dirty coat, and a yellow code aura around his head, stated that he saw a 'dangerous deception' something that he could see because a 'veil had been lifted from his eyes', and that he had a new, more important purpose than guarding the Oracle.
The attacks still continued, but with surprising results. The Cypherites, with their leader, Cryptos, were approached by Seraph whilst on their way to a bluepill that had been attacked. Without warning, Seraph attacked Cryptos, knocked him down, and escaped.
Cryptos began to act strangely, with his glasses and trademark bluepill knocked off, his eyes became black, only showing yellow code on his eyeballs. Blind, Cryptos began to lose control of his speech, calling for fellow Redpills and Veil, the other Cypherite leader. As the Redpills around him tried to aid their leader, he began shouting 'INPUT ERROR, RUNTIME ERROR, OPTIC ERROR'. As Veil ordered her crew in the real to pull his jack, it became clear that he had been a machine from the start, although who he was originally working for is still unclear. It turned out that Seraph only attacked operatives and bluepills that were over-written by the Machines sometime in the past (similar to the Smith virus). Apparently, as a result, Zion is slowly became distrustful of the Machines.
On the Merovingian's side of things, his organization is attempting to get kill-codes to the Oracle's shell once again. His new-found ally, the General, has stated that a cheat code vial is required as an ingredient, and only an Exile called the Apothecary can manufacture the kill-code with the vial. After recovering a vial from a bluepill named Jason Hernandez, looking for the Apothecary was problematic, as the Machines held the Apothecary inside a construct that only the Trainman can reach. As a result, the Merovingian had his operatives search for the Trainman.
It was discovered that the Machines had, since the Truce, been using an ability to over-write thoughts and minds (an ability they discovered was possible after Agent Smith's use) and place programs of their own writing in their place. They hoped that by exhibiting a degree of control over peoples' thoughts and actions, they could better control and thus maintain the stability of the Matrix.
The Machines' plan is nulled, however, with Seraph's permanent return when Zion performs scans on all of their redpill operatives for any indication that they have been "overwritten". It is discovered that a large percentage of Zion's operatives have been "overwritten" by the Machines.
The Cypherites, feeling betrayed by the Machines (and with their "leader" Cryptos still recuperating) turned to their Mission Controller, Veil for support. It is around this time that accusations were made of the Cypherites enjoying a new found love for violence, feelings which may have been stirred by Veil's new found authority in Cryptos' absence and the anger she felt at the betrayal.
===Retaliation against the General===
Seraph, using his new powers, discovered he can detect the General's new Elite Commandos, normally "cloaked" against normal scans within the Matrix, and began assisting Zion to find and rescue Sati.The Machines found the General's base in The Real, code-named "Stalingrad", and launched an assault against it with their own army of Sentinels, only to encounter very strong resistance. To counter the delay, Agents began tracking down and eliminating the General's systems of communication within the Matrix and disrupted his movements. Frustrated, the General was pleasantly surprised by the Merovingian's offer of alliance, under the condition that he help manufacture a kill code for the Oracle.
===The Fall of the General===
The Machines finally defeated the General's Sentinel guard in Stalingrad (Machine code-word for the General's forces' main point of entry into the Matrix), at the same time cutting off all of his modes of communication and transportation. With no steady source of reinforcements, the General was forced to deviate from his still continuing offensive actions.
Seraph aided Zion in its effort of tracking down and rescuing Sati. Once she was freed from the General's men, Seraph returned to the Oracle and protected her as she moved from her usual apartment in the Richland district of Mega City to a safer location, having had word that she may be a target for assassination.
The Merovingian completed the construction of the kill code intended for the Oracle, using Agent Pace as a practice target to ensure its lethal capabilities. Agent Pace was severely wounded in the attack, but repaired quickly and returned to active duty with a much colder and calculating personality, more similar to the standard stereotype of an Agent as had ever before been observed. The Merovingian, however, was quickly side-tracked by the General's position as he lost base after base, Commando after Commando at the hands of Zion and Machine operatives. With the aid of the Trainman, who had earlier assisted the Merovingian with the transportation of the kill code, the Merovingian began shuttling the Commandos into constructs.
Finally, the General's only remaining base of operations is found and eliminated, with the General barely escaping. Surprisingly, he rejected being transported to the Merovingian's construct, stating that he had "unfinished business".
Meanwhile, the transmissions (previously thought of as having been made by Morpheus) are discovered to be originating from somewhere inside the Matrix, rather than Morpheus' hovercraft in The Real as was originally suspected. While many high-ranking officials in Zion are convinced the Morpheus signal was a fake, the signal became stronger.
On June 11, it was revealed that the General was behind the false Morpheus broadcasts by constructing a Morpheus Simulacrum. When confronted by Zion operatives, it was extremely hesitant to reply and spoke with a lack of direction and confidence. The General appeared to terminate what he deemed his failure, but the Morpheus Simulacrum fought back and defeated the General, the General furiously taking of and leaving the simulacrum to come to terms with its existence; that as a copy of the original Morpheus.
With the General's temporary disappearance, the Merovingian again focused his efforts on assassinating the Oracle by planting a redpill mole within Zion's security detail, as well as recovering the Keymaker's chain from a prominent Exile known as the Landlord, at the Mahath Tower wreckage site in Lamar in the Downtown district of Mega City. Unfortunately for the Merovingian, the attempt to assassinate the Oracle had been leaked to Zion due to a communications error. In turn, the majority of Zion operatives focused on investigating the leak and eventually captured the mole, although they did not recover the kill code. The Merovingian then went to the General with a request for aid in the form of the General's "Elite Commandos".
The Effectuator handed out Elite Commando disguises among the Merovingian ranks as a means of confusing the Zion security detail between the real Commandos and those operatives simply wearing a disguise. Before the assassination was to be carried out, the Machines were able to make use of a special surveillance system which could identify whether those seen as an Elite Commando were wearing a disguise; thus rendering the disguises as useless.
A single Commando was dispatched to assassinate the Oracle and moved quickly to close in on the Oracle before she could detect his presence. Again, however, the Merovingian's plans were foiled by the presence of Michael Karl Popper. As the Commando fired the single shot which would herald the Oracle's permanent deletion, the Kid jumped into the path of the bullet, preventing it from hitting the Oracle; (The Kid had not reported any adverse reactions to absorbing the kill code meant for the Oracle). Frustrated, the Merovingian saw it only fitting that he take control of both the General and his men, in exchange for their inability to carry out the assassination on the Oracle by activating override routines secretly implanted in both, during the transfers.
===The End of the Truce===
With help from the Cypherites, the Machines discovered that Zion had been moving heavy pieces of machinery to a large cavern and so dispatched a Cypherite reconnaissance hovercraft in order to investigate further. It was discovered that the cave was filled with stationary EMP devices, at the bottom of which was a shaft which descended through another EMP field. Above the cavern lie impenetrable layers of the earth's natural strata. At the bottom of the shaft is the location of a new city, New Zion, built to house and protect those humans freed from the Matrix.
It was later found that construction of New Zion had begun when Captain Niobe was held in Anome's construct, and that Zion had been constantly adding to its defenses since. Upon the discovery of New Zion, the Architect informed Agent Gray that "No further awakenings are to be allowed", effectively calling an end to the Truce between Zion and the Machines and renewing previous hostilities. Zionite operatives who now venture outside of the Richland district of Mega City are now attacked by patrolling Agents. However, Agents continue to attack those players who have not gained proper access for each area in each district via Access Cards and Access Nodes, regardless of affiliation.
===The Intruder===
In Chapter 9.1 an unknown entity that only goes by the name "Intruder" (takes the shape of a wireframe man with spontaneous code leaking from his frame) at this point in the story has made many recent appearances in the Matrix. This "Intruder" at first seemed weak to normal attacks and even more vulnerable to viral attacks. The Intruder had been shown in a Vector-Hostile event to have the ability to spawn Decelerator spawns that take the shape of a large floating ball of code that constantly uses a debuff ability.
The Intruder also can "take it up a notch" where he inflict 1-hit K.O.'s regardless of the player's level, therefore decimating redpill operatives. Programs are simply futile against the Intruder as he can "override" the programs with an Accelerator or Decelerator program, allowing the program to only do as he wills. The Intruder's intentions at that point were ultimately unknown as the large menace seems to have accustomed to a rash attitude. It is eventually revealed by Agent Gray that the Intruder was a free-born human.
==Story Rumors==
*Neo's ultimate fate has been openly called into question as Morpheus has pointed out that his remains were never returned from 01 (the Machine City) back to Zion, but at the same time the Machines have commented that they did not recycle (liquefy for reuse) his body. On an interesting note, there is a newspaper clipping found during a Zion critical mission about a 27-year-old woman named Sarah Edmontons (an anagram for "Thomas Anderson") waking up from a coma and leaving the hospital on her own. In the text, there was a note written on it asking, "Is this him?" Furthermore, on one Machines' set of critical missions, it turned out that Edmontons does not exist in any known database, therefore supporting the speculation that Edmontons is Neo. Although no outright comments have been made, developers have hinted that Edmontons would have played a role in the future.
** Further rumors of Neo's return sprouted at one point, due to the Machines placing Neo's supposedly partially reconstructed RSI in a fight club in Gracy Heights in Westview. This fueled the idea that Neo was still alive; however, many Redpills believed that the RSI is simply a distraction from Neo's ultimate fate.
** There have been recent (as of April 2007) appearances of Morpheus' signal within Megacity, claiming that Neo is still alive someplace and that the Machines have him.
*Excerpts of a "journal" written by the Assassin claims that it was a program in charge of recycling [of human corpses in the power plants] before it went rogue to become an Exile program. They claimed that while the Assassin was still in charge of recycling, it received a command expressly forbidding it to recycle Trinity's body.
*In a Machine critical mission, operatives were informed of the origins of the General. It was revealed that when leading the final attack on Zion, he wanted to continue the attack, even after the truce had been brokered, disobeying orders. Forcibly removed from command, he was put into another post but instead chose to become an exile in the Matrix, utilizing a terminal on the surface to gain access; with no foreseen need for an administrative override function, bringing his commandos with him.
*It is commonly suggested that Agent Smith still exists within the Matrix. Most of these have come about from the various hints that were communicated through the Live Events. For example, on the Syntax instance, former liaison officer DifferenceEngine had to be arrested following his apparent infection (notable from his vocabulary). Further fuel was added to the fire through various hints that Agent Gray, the Machine mission controller, is infected, notable from one of the critical missions in the Hunt for the Assassin event where he possessed the tell-tale vocabulary and acted with un-program-like anger. In addition, Shane Black on the Recursion instance was seemingly taken over by the Smith program, as suggested by his vocabulary, though this was only a resurgence of memories from his previous Smith infection, brought on by observing Unlimits fighting in the Aqueduct. He was later killed.
*Another Liaison officer, TaeCross from the EPN's Recursion instance, was rumored to be working with Morpheus a full year after his last known sighting. After poor dealings with the Machines and repeated setbacks, TaeCross acted out in a Morpheus-like attack of code bombs on the city. It was strongly rumored that since the code bomb technology hadn't been seen since Morpheus' disappearance, TaeCross got this technology directly from Morpheus himself. TaeCross unleashed a final set of 8 code bombs simultaneously at the steps of the First Union Church in Camon Central. His final whereabouts were left unknown. It is also of note that TaeCross is an anagram of Socrates.
==Ending==
The game officially ended on July 31, 2009 with all player characters seemingly dying simultaneously.
==Developer File Dump==
After the confirmed discontinuation of The Matrix Online, story developer Rarebit released a file dump of his complete planned story arc for the released, and unreleased, chapters of the game. He stated that these plans had been subject to change and modification and were simply a rough projection--however these notes are now all that exist for the closing chapters of the MMO. There is also some interesting background information revealed from previous chapters as well, therefore the full file dump is being presented in its original format: The Matrix Online Archives.
====1.1====
Introduction to the Matrix under the Truce.
====1.2====
Morpheus begins a campaign of protest and sabotage to force the Machines to return Neo's body. Zion declares Morpheus' actions a threat to the Truce. Mysterious, hostile groups begin to appear in the simulation: imposter Agents with red eyes, and groups of operatives with masks concealing their faces.
====1.3====
Morpheus is killed by the Assassin, an exiled disposal program in form of a fly-filled overcoat and porcelain mask. Niobe brings her own group of operatives into the Matrix, along with her new right-hand man, Anome, to bring Morpheus' killer to justice.
====2.1====
Niobe finds out that it was the Merovingian who hired the Assassin. Operatives begin to gather insecticide spray to fight him.
====2.2====
Insecticide-spraying flit gun weapons are assembled to fight the Assassin. He is found to move through phone lines, and reside on a garbage barge. The red-eyed Agents vandalize phone booths. The masked men are lying low.
====2.3====
An exiled program, the General, appears with his Commandoes in a helicopter, with offers of help for the various organizations. The Assassin's power grows, but he is tracked down and killed.
====3.1====
Niobe seeks revenge against the Merovingian for the death of Morpheus. The Machines are also working against the Merovingian. Mysterious hissing and creaking boxes appear around the city.
====3.2====
The masked leader, Cryptos, appears from the hissing boxes, preaching a return to sleep in the Machine pods. The name of the masked group is revealed: the Cypherites. Their agenda is opposed by the other organizations.
====3.3====
The General joins Niobe and Zion against the Merovingian. Cryptos' past as a fervent anti-Machinist, and friend of Morpheus, is revealed.
====4.1====
Zion uses kill-codes provided by the General to combat the Merovingian's Exile programs, and searches for Cryptos' base of operations.
====4.2====
The Kid gathers like-minded operatives and leaves Zion, forming the group "E Pluribus Neo", aka "EPN", to counter the Cypherites. The Merovingian develops weapons to kill the General's commandos.
====4.3====
The General points out powerful "Cheat codes" to Niobe, carried across the city in a locked case. He has the key, but Anome fumbles it into traffic. Everyone scrambles for the key and the case. Zion obtains them.
====5.1====
Niobe opens the cheat code case, but is betrayed by Anome, who steals the cheat codes, shoots Niobe, and uses one of the codes to trap her in a pocket construct. Everyone tries to stop Anome. The Merovingian offers to help Zion rescue Niobe: his construct specialist, the Effectuator, is at their disposal.
====5.2====
Zion finds and rescues Niobe with the help of the Merovingian and the Effectuator. The Machines and the Merovingian begin tracking down and killing Anome's lieutenants, who have become super-powerful by ingesting cheat codes. The General is chased out of the Matrix by the Machines.
====5.3====
Anome formally names his group "Unlimit". Unlimit begins attacking city facilities, particularly those belonging to mega-corporation Pendhurst-Amaranth, whose representative Brenda Utley calls on Zion for assistance. The Merovingian captures Beirn, an Unlimit lieutenant obsessed with Persephone.
====6.1====
Unlimit kidnaps Brenda Utley, and moves to take over Pendhurst-Amaranth. The Machines learn of Anome's past, and his psychological weakness, from an Unlimit member, Meillak, whose friend Caboclo was tortured and killed by Anome for questioning Unlimit's threats to innocent civilians. The Merovingian uses synthesized cheat codes to restore the Twins. E Pluribus Neo rescues Brenda Utley from Unlimit.
====6.2====
Anome is killed by Agents. The Machines ask for access to Zion's mainframe, to help head off security threats. Zion learns that the Machines have a massive Sentinel force ready to strike Zion. The Cypherites offer to infiltrate Zion for the Machines. Zion refuses to give the Machines access. The Architect orders increased surveillance and infiltration of Zion. The Merovingian quashes a Exile rebellion in the slums, and discovers that the General's commandos have been active there.
====6.3====
The General kidnaps Sati. Seraph disappears into the river while trying to rescue her. The sky begins to turn red. Agents dump cheat codes confiscated from Anome into the river, but one lodges intact under the pier. Zion combats the General and his new "Elite Commando" stealth programs. The General reveals to Zion that he was the commander of the Sentinel attack on Zion just before the Truce. The Machines begin shutting down the General's access points inside the Matrix, and find out that he has a base on the Earth's surface, code-named "Stalingrad". The Merovingian makes a deal to assist the General in exchange for the General's help in making a code to kill the Oracle.
====7.1====
Seraph crawls out of the river, and attacks people around the city. Zion finds out that these people were overwritten by the Machines, and that Seraph, affected by the cheat codes in the river, can cure them. After months of rumored sightings, Morpheus appears in the Matrix, delivering a broken message suggesting that the Machines are holding him and Neo captive. Sentinels close in on Stalingrad while the Machines develop ways to counter the stealth techniques of his commandos.
Seraph attacks Cryptos, revealing him to be overwritten by a Machine program, and leaves him in an incoherent state. The General helps the Merovingian locate the last cheat code vial, which he says will be needed for the Oracle's kill-code. The General tells the Merovingian that a Machine program known as the Apothecary can make him an Oracle kill-code, but the Trainman is needed to bring her into the Matrix. The reluctant Trainman is found hiding in his subway construct. The Machines begin receiving reports from Cypherite spies in Zion.
====7.2====
Seraph, restored to normal by Zion, helps them locate and rescue Sati. Morpheus appears again, but erratically; he is clearly a program, not the real Morpheus. Machine and Commando Sentinels battle at Stalingrad. The Machines shut down the General's network in the Matrix. Cryptos recovers and asks the Machines to reinsert him into the pods; they tell him no such procedure exists. The Trainman brings the Apothecary into the Matrix. After testing against the Machines' Agent Pace, the Apothecary develops an Oracle kill-code for the Merovingian; he allows the Apothecary to be killed by hostile operatives. Spy reports from Zion show that men and material are leaving the city.
====7.3====
The sky returns to normal. The Machines level Stalingrad. Zion and EPN discover that "Morpheus" is a simulacrum created by the General, based off of recorded pieces of the real Morpheus' speeches. The Merovingian sends a specially-equipped commando to kill the Oracle, but he is stopped by the Kid and EPN. Zion finds out about Cypherite spies in their city. The Merovingian hides the General in his white hallways, and stores some of the commando programs away in hidden constructs. The Machines badly wound the Merovingian's transporter, the Trainman, who disappears.
====8.1====
Cypherite spies discover that Zion has built a new, strongly defended city. The Machines declare that Zion has broken the Truce. Open hostilities between Zion and the Machines begin. The Merovingian, skeptical about the Morpheus simulacrum's story of humans used as batteries, sends his commando Sentinels to scout the Machine "fields" and pods.
====8.2====
Zion turns to ex-Zionite specialist Danielle Wright when the Machines compromise their red pill program. Wright develops a new, secure pill for Zion, but is killed by the Machines, who use her hidden, direct access to Zion to insert a virus into Zion's mainframe, while a Cypherite spy destroys Zion's command center with a bomb. The Merovingian finds that the Machines do rely on humans for power, with regular pod centers across the otherwise barren surface of the planet, and have barely enough energy to run the Matrix and their own city.
====8.3====
Sentinels attack Zion's crippled city, forcing Zion to abandon it. Zion's Commander Lock is missing. Roland, whose ship was destroyed in the attack, is promoted to replace Lock. Roland's crew member Colt becomes a Zion captain; another crew member, Mauser, thought to have been killed, is seen on Sentinel surveillance tapes helping Lock escape through rubble in Zion. The Machines use data captured from Zion's mainframe, unlocked for them by the confused Morpheus simulacrum, to hunt down and kill veteran Zion operatives. The Merovingian finds evidence of the Machines removing live humans from the pod system.
====9.1====
A glowing "intruder" appears in the city, instantly killing Agents who try to stop him. He wants information from Zion. The Machines pull back their forces in the Real, and try to prevent the intruder from making contact with Zion, but refuse to attack him directly; they eventually admit that he is a freeborn human, with some direct control over the Matrix through "override codes." The Merovingian tries to win the intruder over. Pluribus Neo moves into the wreckage of Zion's old city.
====9.2====
The intruder pumps Zion for information about their history. EPN begins to fortify Zion's old city, and find Commander Lock lying wounded in a hidden lab at the surface. Lock says he was saved by Mauser, who died defending him from Sentinels. The Machines try to convince the intruder to leave. He becomes increasingly frustrated, and demands that the Machines give him a "Biological interface program." They claim that only one exists, and it is not in the Matrix. The Merovingian searches for programs the intruder might be willing to trade for, without success.
====9.3====
A second glowing figure, Carlyne, enters the Matrix, attacking the first intruder, Halborn. The Morpheus simulacrum contacts Exiles in Westview. Halborn learns from the Machines that the Oracle created the program he seeks, and pursues her. He is supported by the Merovingian, and opposed by Zion, who have help from Carlyne. The Oracle contacts EPN and the Cypherites, giving each group part of an encrypted program, and asks them to watch over Sati. Halborn reaches the Oracle, who refuses to help him, and kills her.
====10.1====
Sati, Seraph, and the Morpheus simulacrum have disappeared. Halborn continues his stubborn search. The Machines turn him over to the Cypherites, who lead him to the spot in the Real where EPN is handing the recovered Lock over to Zion. Halborn flees the large hovercraft battle that ensues, but his ship was noticed by Zion, who, with EPN, defeat the opposing ships, and take Lock to their new city.
Following a chance remark by Halborn, the Merovingian, using the General and his Sentinels, locates a "no-fly" area far to the northwest of the Machine city, avoided by Machine patrols, where they find a heavily defended facility, and a data feed from a massive "Oligarch Network". Zion and Carlyne succeed in surprising Halborn and removing him from the simulation. Cryptos begins research on anti-override codes. Carlyne leaves the Matrix.
====10.2====
Mauser, who never had jacks, appears in the Matrix. He hops through unmarked hardlines, avoiding contact, saying to Zion only that he's working to win the war. The Merovingian seeds the storm between the Machine city and the no-fly zone in order to reestablish contact with the General. They find Oligarch network data flowing into the Ouroboros Corporation in Downtown. The Machines nearly isolate Mauser's signal, but are interrupted by the Morpheus simulacrum. Mauser steals data from the Merovingian, then disappears. Missile barrages devastate the General's forces in the no-fly zone, forcing him to retreat. EPN detects a small craft outbound from tunnels below the old city, heading north.
====10.3====
Cypherites find the Merovingian hacking into Ouroboros. Cryptos captures some of the Oligarch data to assist his research. EPN discover data that was left behind on the no-fly zone at the small craft's launch site, and begin to prepare ships of their own to investigate. Machines try to get the Merovingian out of Ouroboros, concerned that trouble there will bring more Oligarchs into the Matrix. Wright Research sues Pendhurst-Amaranth for a break-in by Mauser. Pendhurst-Amaranth's Brenda Utley helps Zion get information about Mauser's activities, but Seraph appears, and asks them to stop. The Merovingian finds the biological interface program inside Ouroboros' network.
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