When we see Smith take over Bane’s consciousness in the real world, we think we’re seeing something new, but we’re not. As we learn from the Architect, Neo is already an example of the exact same thing: he is a real human implanted with machine code that enhances or completely changes Neo’s consciousness.
Agents are sentinels (see Matrix System: Agents), and the Smith virus controls Agents of the system (we see Smith take over an agent during the Burly Brawl). The Smith virus therefore has some control over the sentinels, which is likely why Bane-Smith was the only survivor of the sentinel slaughter at the end of M2. Even if not, machines sense each other through the Source (how? see Neo's Powers: Blind Sight), and the sentinels would have seen the fiery Smith figure when looking at Bane-Smith, the same figure Neo saw just before beheading Bane-Smith. Deux Ex Machina might have been able to tell the sentinels to spare Bane-Smith's life since their goals of killing humans were aligned.
To understand why Bane-Smith went into a coma, it is important to first understand why humans cannot be jacked into the Matrix while an EMP is set off. An EMP effectively "turns off" all of the ship's equipment, accomplishing the same thing as unplugging a human while they're inside the Matrix, abruptly cutting off the Matrix feed. But even if an EMP didn't shut off the equipment, remember that the plug in the back of the human's head is electronically active when they are in the Matrix. This means that humans themselves can be "disabled" by an EMP when their headplug (which is connected directly to the brain and the spine) is active.
After Smith took over Bane, it is very likely that the Smith program interacted with (or even resided in) Bane's headplug, continually hacking Bane's brain. When Bane-Smith set off the EMP, it would have instantly "disabled" Bane-Smith because of the active headplug. Thinking of Bane's body as a "machine" that is disabled by an EMP, such machines must be "restarted", the same way Trinity restarted the Logos after the electrical clouds disabled the ship. Fortunately for Bane, he is a human whos "power supply" is not dependent upon metallic electrical circuits. But unfortunately for Bane, the Smith program (possibly residing in the headplug) also has access to this same human power supply. So, immediately after the EMP, as Bane tries to retake control of his own body, the Smith program would resume preventing Bane from taking over his own body and continue hacking Bane's brain. It would only be a matter of time before the Smith virus succeeds at retaking control over Bane's consciousness.
If this is true, why didn't the EMP kill Bane-Smith instead of just putting him into a coma? It is because Bane's RSI (or just consciousness) is still inside of his own body. His consciousness is not being broadcasted out into a Matrix or computer simulation (and left to die in the simulation). It was merely the interruption of his interaction with his own headplug that caused Bane to go unconsciouss. This "interaction" consisted of nothing more than the Smith program hacking his brain.
The EMP did physically damage Bane's brain, however:
Roland: Has this man been tested for VDTs?
Maggie: Yes, sir, it was negative. But he is showing a lot of unusual neural activity. Some cross-synaptic firing as well as signs of recent trauma, with fresh fibrotic scarring throughout the cortex.
First, VDT is probably form of delirium tremens. Delirium tremens consist of tremors and hallucinations (often rats, insects and snakes) caused by severe alcohol withdrawal. VDT would likely be caused by withdrawal after unplugging from the Matrix - thus, "Virtual" Delirium Tremens. Maggie mentions VDTs in a previous scene when Bane-Smith is still unconscious, suspecting that VDTs are responsible for his self-inflicted cuts.
A synapse is a path by which brain cells communicate with each other and also with non-brain cells such as muscle and gland cells. Synapses are critical to supporting perception and thought. So, when Maggie says there is "cross-synaptic firing", to me this sounds like Bane's consciousness is trying to reinstate itself, while the Smith program is trying to block Bane and take him over again. The "fibrotic scarring" was probably caused by the EMP "short-circuiting" Bane's brain.
Smith is the “Bane” of Neo’s existence. More generally, we could also say that Smith is both "the Bane of one's existence" and "the Bane of One's existence", since Smith threatens mankind as well as the One.
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