Sparr. I think it goes deeper then that. Neo waas ablt to stop the sentinels outside the matrix just like he was able to stop bullets inside the matrix. I think that what the zion people consider to be the real world might even be a second matrix and that the matrix only is a matrix within a matrix. The architect was also outside of the matrix, yet the digital neo could also exit the matrix into the architects room. That room has to still be a computer program then. The fact that that special 63rd(?) floor exploded might also mean that the control-area of the matrix is destroyed. Maybe the matrix is out of control and cannot be shut-down without chrashing the computer-system that runs it. That could explain why there will be an 'after-movies'-matrix.

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