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Location: in between Trinity's buttocks
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Theory 1
"You touched the Source, but you weren't ready"
To begin with, she does not immediately say: "you touched the Source, so you should be dead"
He wasn't ready? Ready for what? The overwhelming power that is the Source. He was surprised by his own deed (which was connecting to the Source and shutting down the Sentinels with the power of his will).
So, he did his deed, but he was overwhelmed by it, coming into some sort of shock. As a result he did not pull back his mind from the Source but was overflowed/overwhelmed by it.
Then the Sentinels went dead, loosing their connection to the Source in the process. Neo did not straighten his mind yet, so what happened was about the same what would happen when someone inside the Matrix suddenly gets his plug removed....and hey...that gets us to the part of: "you should be dead..."
And offcourse Neo didn't die by this, because...
A) He is the One
B) His strong will for the love attachment
Theory 2
Neo connected himself to the Source, which tried to assimilate him. By the power of his will, Neo managed to escape to Mobil Ave.
Both theories are plausible, but alot of questions are still pending, especially with theory 2, let me elaborate on them...
1) Did he still need his physical brain to have his conscious experience in Mobil Ave or did the Source assimilate everything from his brain, including his entire lifetime memory and turn him into a full AI-program?
I think the latter doesn't make sense at all, because...
A) If the Source would want to delete him, then why the hell would they make a stand-alone program out of him in the first place?
B) The RSI is a 'replacement' for the five senses of the physical body that normally feed the brain with information. This information comes from the simulation in which they participate in. Throughout the trilogy we are being told that the RSI and the physical brain cannot be seperated in any way, they operate as one.
This proofs for me that Neo needed his physical brain in order to be a conscious entity inside Mobil Ave, unless he or the Source did some magic alterations and converted him into a stand-alone AI program. Even if this is so, then the Source must have done this, because Neo doesn't even know how he got into Mobil Ave in the first place (like he says to Rama Kandra).
But Rama-Kandra says that perhaps Neo is there for the same reason as he is: a love connection! This might imply that it was Neo's will to 'escape' from the Source into the save 'island' that Mobil Ave is.
So this is confusing stuff. On the one hand Neo doesn't know how he got there and on the other hand it is suspected that he is there because of his strong will. This might indicate that this will is expressed through his subconscious part of his mind, which I described earlier.
2) If Neo can connect wireless from anywhere (like some of you think) then why did he went unconscious in the first place? Both his physical body and his RSI went unconscious.
In the original draft of M3 it is described that Neo wakes up in Mobil Ave with a tremendous headache. This is proof to me that his first connection with the Source was too overwhelming for him.
So for me theory 1 comes the closest...summarising:
-Neo connects to the Source for the first time
-The Source's power is overwhelming for him causing some sort of shock
-The Sentinels loose their connection to the Source
-Neo straightened (disconnected) his mind too late, leaving it at the Source
-By his (subconscious) will Neo wants to return, so he flows to the first possible exit: Mobil Ave station
-Inside the Hammer, again with his subconscious will, he re-establishes the connection between his RSI and his phycial brain, giving us two visual clues about this: Maggie spotting certain patterns on him and his RSI waking up
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