This question relates to the movie : Matrix Revolutions
In this third installment, we see Neo, in the real world, fighting Bane. Bane's mind has been replaced by Agent Smith. Bane, in his head, is Agent Smith.
Bane blinds Neo, Neo's eyes in the real world are burnt. Neo, after loosing his eyes, begins to see the world in a golden glow. He sees Agent Smith instead of Bane.
Let's park the idea of matrix within the matrix idea because that invalidates the whole trilogy. That invalidates any knowledge of how the current world looks like. That also gives rise to infinite possibilities and explanations to what is actually happening in the real, real world.
Assuming that the real world is indeed the real world, how does Neo begin to see with the golden glow? I'm looking for a scientific explanation, not a spiritual one.