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The Assassin was a shadowy killer charged with the killing of Morpheus after his use of code bombs to kill mass numbers of bluepills in a terrorist agenda to force the Machines into returning the body of Neo, The One.
Originally a waste recycling program, the physical form of the Assassin was a humanoid mass of flies within a full length trench-coat, black gloves and white porcelain mask. This amorphous form not only gave him tremendous advantages in a chase (for example slipping through ventilation systems) but it made him incredibly hard to kill. It was not until it was revealed that his insectoid composition left him with an extreme vulnerability to insecticide that a plan could be put into motion to eliminate him. In a climactic battle on a garbage scow off the coast of the Mega City, Zion operatives were finally able to kill him. Like many powerful programs, however, his data has not been completely purged from the System, and from time to time echoes of his code tend to reoccur.