The Hunt for Morpheus event in The Matrix Online began with the disgruntled Morpheus resorting to drastic measures to coerce the Machines into giving up Neo's remains. Empowered with a new mission, Morpheus set off bombs around The Matrix MegaCity. These code bombs threatened the fabric of the Matrix, releasing a virus that would show humans' "reality" and potentially crash the whole system.
Predictably, there quickly followed a ferocious effort to stop him. The Assassin appeared in the Matrix, sent by... someone... to kill Morpheus. The Assassin finally caught up with Morpheus in a waste water treatment plant - which is significant.
Morpheus had finished planting his latest code bomb when he sensed an unusual presence. A buzzing fly betrayed the porcelain-masked Assassin, who took his first shots at Morpheus. Morpheus dodged by jumping over a walkway rail and escaping down a dark alley. As Morpheus fled, the Assassin fantastically flowed through a small vent directly in front of Morpheus. Somehow, the Assassin could bend the rules of the Matrix.
Morpheus was caught off guard and had nowhere to flee. The Assassin opened fire, catching Morpheus in a hail of bullets that even he could not dodge.
It seems impossible to believe - Morpheus is dead.
Matrix Online
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