The Matrix Online continues the story of the Matrix. So far (from what I played) Morpheus want's Neo's body, but the machines won't give it. So he sets off code bombs to make the blue pills (people living in the matrix) what they really live in. Later Morpheus is killed by an assassin that can somehow "bend the rules of the matrix" which blue pills cannot do. Last I checked they were doing the "Hunt for Morpheus' Assassin" I haven't checked recently.