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First, the war is to save the last city of humans, Zeon. Neo is learning more of his powers but he is indeed powerful. Agent Smith has cloned himself multiple times to seek vengeance. Neo's biggest enemies will be these two men called "The Twins" ! I read they are virus that have be given the permission to resurect . They are like ghosts and can appear and disappear everywhere, anywhere they want...
We also see Morpheus' ex-girlfriend (the girl with black long hair...). She owns a hovercraft like Morpheus and leads her own war too !
Aside from that, Neo's relationship with Trinity will expand throughout the movie...
That is all
TigerLord