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I always thought that he could get hurt in the matrix, for example if a bullet hits him he will get injured. Otherwise why bother to stop the bullets from reaching him? Why waste his time stopping the bullets? Why not just build a "firewall" around himself, and not worry about any dangers in the matrix? Answer is that he can be hurt by the matrix even though he can manipulate it. For example if a nuclear bomb were to go off next to him he would die.
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