The Smith Virus in The Matrix Online
Despite his destruction at the end of the film series, Agent Smith (or at least the remnants of his programming) managed to return and made several appearances inside the movie's official continuation, the MMORPG The Matrix Online.
The first infection was noted in Machine mission controller Agent Gray, whose background information confirms that he was overwritten by Smith at some point during the timeline of the second and third films. This infection had somehow survived the reboot at the end of the third film and rose to the surface once again during chapter 1.2, The Hunt For Morpheus. The Agent, in both a storyline related mission and live event, showed signs of uncharacteristic speech and emotion and eventually led an assault against Zionist redpills declaring 'their stench unbearable any longer'. As a result of his actions the agent was apprehended by his fellow system representatives and scheduled for a 'thorough code cleansing'. He has shown no signs of direct infection since.
Machine liaison officer DifferenceEngine, following a similar scenario to that of the previous Agent Gray infection, also took on the dialect and emotional characteristics of the famous exile agent. Instead of attacking redpills, this instance insisted on finding 'Mr. Anderson'. In the end, the human/machine head relations liaison, Agent Pace, was made aware of the program's infection and subsequent crusade; she proceeded to lock down his RSI and return his program to the Source for analysis. His subsequent fate is unknown.
The third victim of infection was the notorious bluepill Shane Black. This man was an unfortunate victim of the Smith Virus who, once infected, gained the ability to spread the code to others. This quickly led to a small scale outbreak, with several more bluepills becoming infected and joining forces in their hunt for power. He and the other infected were eventually cleansed and returned to their bluepill lives. Shane Black's troubles continued, as he was one of the bluepills recorded to have first witnessed Unlimited redpills practising their newfound powers at the Uriah wharf. This triggered a resurgence of the memories formed during his Smith infection and he soon became volatile and insane. He is reported to have been mercifully killed shortly afterwards.
The most recent appearance of the Smith virus was during the third anniversary events. The virus manifested itself in the form of black-suited men (although they lacked the distinct likeness of Smith). As redpills began to fight back using specialist code from the Oracle, the virus vanished suddenly, stating that he had obtained a new and more dangerous form. The only person to kill the main Agent Smith virus was the Machinist Trilateral, originally of the Iterator server, on Recursion server after the server merge, being the first person in game to earn the perpetual flame virus award. The nature of this form was never revealed.
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