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Questions, When Neo at the end appeared to stop the machines, are you sure he did? Maybe the ship that rescued them released an emp just as Neo raised his hand, giving the impression Neo was responsible.
thats possible, but how do you explain the feeling he talked about when they came. it would be too coincidence. although it did look kinda like an emp blast like from the first movie it would still be too coincidence. i think he accaully did stop them. i think something new is fixing to happen.