In M3, we see the world through Neo's "blindfolded" eyes as a kind of virtual reality consisting of glowing yellow representations of machines and their
structures. The vast majority of those who see M3 for the first time feel frustrated at this point, because it feels as if we are being asked to believe
that Neo can see better without his eyes by some miracle of God. But there is no miracle here.
Going all the way back to M1, we see that Neo can "feel" the machines. He says it in the phone booth at the end of M1, he says he can feel them even more directly in M2, and of course the Oracle tells us in M3 that Neo derives his power from the Source. One of the senses Neo is surely "feeling" is the reception of projected machine images from the Source. Neo sees machines the same way sentinels and other machines see each other. Think of it as if all machines carried enhanced GPS devices that allowed a control center (the Source) to track the positions of all machines, therefore enabling every machine connected to the Source to see other machines.
Neo didn't gain this ability from being blinded - he gained it when he entered the Source. His eyesight was actually getting in the way of fully experiencing his new connection to the machine world through the Source, perhaps because his brain didn't know how to process multiple spacial awareness senses at once.
Sentinels and other machines have special lenses allowing them to see more than just each other. In "Matriculated" (The Animatrix), the "runner" machine can see a human running even when the human goes behind a hill, because the machine has extra sensory devices devoted to perceiving the surrounding environment. However, Neo doesn't seem to have such vision devices, and his vision also has other limits. Neo couldn't see his own ship or Trinity, so Neo was still visually "impaired".
Notice that when Neo sees Bane after being blinded, he doesn't see Bane - instead, he sees a slightly inaccurate flaming version of Smith! When machines broadcast their real world positions to the Source, they aren't just sending (x,y,z) location coordinates. They are sending the same thing that is communicated and utilized within the Matrix: RSI (see Introduction: People, Places & Things for a definition of RSI). Smith cannot project his RSI into the actual real world because there is no "Matrix within a Matrix" (Trinity still sees Bane). But Smith's RSI is still being projected back to the Source, which Neo is connected to. Therefore, Neo is receiving the rough RSI image of Bane-Smith from the Source.
Everything Neo sees in the real world consists of some kind of beautiful gold-colored entity. Everything except Bane-Smith. Why does Neo see Bane-Smith as a flaming Smith instead of some kind of gold-colored image that looks like a machine?
When the Source broadcasts RSI images in the real world, it makes sense that it would broadcast various types of entities with a different look, the same way a GPS system might broadcast blue dots, red dots, yellow dots, etc. to represent different types of cars, planes, etc. The system is able to spot exiles readily and quickly while inside the Matrix, so my guess is that exiles are spotted just as easily outside the Matrix (so the flames represent Smith's exile status). But consider that Smith's exile status is not the only thing that makes Bane-Smith different. There are actually three qualities that set Bane-Smith apart from other entities Neo sees in the real world:
What a unique entity Bane-Smith is! One sentinel would probably say to another sentinel, "Look at the human exile virus - you don't see one of those too often." Each of the above differences (human, exile, virus) may actually have contributed its own unique visual effect to the the overall look of Bane-Smith's RSI.
How does Bane-Smith project his image back to the Source if Bane is just a normal human (not a special human like Neo)? The only reasonable answer is to say it is the headplug that every Matrix-grown human has. The Smith program knows how to utilize this headplug while conciously awake (as does Neo subconsciously since he is the One). Normal humans, when awake in the real world, apparently have inactive headplugs since Neo cannot see Trinity in the real world after he is blinded (Trinity's headplug was inactive).
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