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After the burly brawl, Neo conviens with Morpheus. He talks about how Smith tried to copy onto him.
"It felt like I was back in that hallway. It felt like I was dying."

So, we can assume that Neo was aware of most everything when his heart stopped and he died. And something else I just noticed... He heard trinity, even when he was Jacked in. She was out, he was in. Odd.

Why is it odd? She is speaking to his real ears. So therefore his brain will still process it.

Once you are plugged in, the brain still functions inside and out.

ooo. I didn't know this

Hmmm, so in Reloaded, Trinity could hear Link say "He's alright, keep moving" when the Twins and their SUV blew up, and that's when she said "Let's Go!" in confidence?

i wondered about that bit

Same, but the body cannot live without the mind. True

didnt she have an ear piece in at that point and had radio contact?

but I can also agree that it would make sense and be cool if she could hear him.

no she didnt, after that she phoned link to ask for a download... you are handy!

if you could hear from the ship then morpheus, trinity, neo, switch and apoc would've heard cypher!

i dont think neo actually heard her

Neo's subconscious heard her, and that was all that was necessary for Neo to wake up...