Thousands of fly swarms have infected the Megacity sky to the point where you canít even see the clouds. Corrupted spawn around the city again and attack everyone, and the flies begin spreading a virus. Unstable code fragments are dropped by the Corrupted that show an ongoing memoir of the Assassin. Zion and Machines decide to form a temporary alliance to solve the code fragment puzzle. The Merovingian is less cooperative since the Assassin was once their ally, but lupine (werewolf) leader Ookami joins the alliance without the Merovingianís consent. The Assassin leads an attack against Ookami, probably because she joined the alliance against him. She is defeated and barely escapes with her life. This causes Flood to announce on behalf of the Merovingian that all exiles and Merovingian redpills are to assist Zion and Machines to destroy the Assassin.
Seraph appears and spreads the word that the Oracle wishes to address everyone about the current situation (the meeting takes place at Debir Court, the same place Neo met with the Oracle in M2. The Oracle says that the flies are spreading a virus that will eventually stress the Matrix beyond its ability to self-repair, and that all organizations absolutely must work together. Feeling the threat against his existence, the Assassin joins the front lines of battle with his Corrupted and kills anyone who stands against him. Flit guns havenít yet been distributed, so there is nothing anyone can do.
The Assassinís direct involvement with the conflict has strengthened the virus itself, and this new virus corrupts the RSIs of redpills themselves, turning them into a mass of flies only kept stable by a mask similar to the Assassinís. Niobe, Agent Pace and Flood each hold meetings with their own operatives, encouraging them to continue unlocking secrets in the code fragments. They also say that the flit guns are almost ready to be distributed.
Finally, the flit guns are ready for mass distribution. All redpill players collect a weapon from one of several distribution centers around the city. Despite the fast movements of the Assassin, he is no match for the combined efforts of all three organizations. He is brought to near death several times but still manages to escape. As a final desperate measure, the Assassin somehow splits himself into 4 separate beings, and they take refuge at the places hinted at by the corrupted code fragments (Club Avalon [inside], Uriah wharfs, the Sobra Shores abandoned subway and Church of the Disciples). The final showdown takes place, and all four Assassin duplicates are killed. All players delivering the final blow are awarded copies of the Assassinís mask by Seraph himself as a gift from the Oracle.
Despite these deaths, Corrupted continue to spawn and flies continue to swarm. Niobe searches the Assassinís barge in case some part of the Assassin managed to survive, and unfortunately her suspicions are correct. The Assassin surprises Niobe by bringing a gun to her head, but an unknown redpill arrives and delivers the finishing blow against the last Assassin. His corruption still lingers, sometimes strong enough to take the form of dead flies. Operatives are sent on missions to clean it up and are rewarded with a fly in amber as a memento. The skies finally clear.
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