I believe a connection with the Source is established as soon as Neo enters the Architect's room (I support this in the Neo: Altered Consciousness page). In M2, there are certain clues that cause us to suspect a connection between Neo and the Source:
These clues are confirmed when Neo speaks to the Oracle in the third movie:
Oracle: The power of the One extends beyond this world [the Matrix]. It reaches from here all the way back to where it came from.
Oracle: The Source. That's what you felt when you touched those sentinels, but you weren't ready for it. You should be dead, but apparently you weren't ready for that either.
Neo did not need to physically shock or EMP the sentinels to destroy them - he only needed to communicate with them through the Source.
From the machine point of view, Neo's purpose within the system as the One is to cancel out rejection and start the next Zion. When Neo chose the left door, both of those purposes failed. As I discuss on the Neo: In Mobil Avenue page, Neo landed in Mobil Avenue the first time because when he connected to the Source to destroy the sentinels, the system detected that Neo himself is an exile and tried to delete him. He "wasn't ready" to be deleted, which landed him in Mobil Avenue.
The second time Neo destroys sentinels and sentinel bombs on the way to Machine City in M3, a sentinel fights back with countermeasures by hacking Neo's mind and making Neo feel that a sentinel is flying through his body. Neo appears very shaken from this agonizing experience, but why doesn't Neo land in Mobil Avenue a second time after apparently connecting to the Source?
The movies unfortunately don't provide a direct answer to this question, but the most reasonable answer to me lies in a clue we get from the Oracle when she says that Neo "wasn't ready" to touch the source the first time. The second time, he was ready, meaning he could guard against the system's attempt to put him in Mobil Avenue the same way he can stop bullets in mid-air. A second explanation could be that the system recognized that it cannot delete Neo and that putting him into Mobil Avenue also didn't work, so the system guarded against Neo with extremely painful countermeasures instead of with a simple attempt at deletion.
At first I was compelled toward a more interesting answer to this question: Neo does not land in Mobil Avenue the second time because the sentinels and their bombs are being controlled by Smith rather than by Machine City. Remember that agents are sentinels (see Matrix System: Agents & Hacking), and at this point we know that Smith has taken over all of the Matrix. In fact, Smith infiltrated Matrix agents way back in M2 when he copied over an agent. Even more than that, remember when Smith was Agent Smith, he was an Arch Agent (again see see Matrix System: Agents & Hacking), commander of all other agents and therefore sentinels. This would compel us to believe that Smith has taken control of all sentinels at this point. Machine City at this point would be inclined to allow Neo to still use his connection to the Source since both Machines and Neo are fighting Smith, their common enemy. The countermeasures we see could be Smith's own doing, his own custom-hacking program designed just for Neo. This would have been a beautiful explanation for why Neo is not landed in Mobil Avenue the second time he destroys sentinels, because at this point the sentinels would be operating with their own rogue Smith code instead of their original programming.
Unfortunately, this theory breaks down by observing the fact that when Neo makes his bargain with Deus Ex Machina toward the end of M3, when Smith has taken over literally everything in the Matrix other than Neo himself, Deus is still able to order all of the sentinels to cease fire while Smith and Neo battle it out. Had Smith been in control of sentinels, he wouldn't have told the sentinels to stop slaughtering all of those disgusting meat sack humans until Smith is done fighting Neo. Apparently, Smith (as opposed to Agent Smith) no longer has authority to command sentinels since such commands must presumably be sanctioned by a connection through the source, a connection Smith no longer has accees to.
Right after that countermeasure is carried out, Neo immediately senses that going into the clouds will destroy the sentinels since the sentinel's hacking of Neo's mind also gave Neo information about sentinels' programming and weaknesses. At that point, Neo tells Trinity to fly the Logos up into the clouds. The sentinels, being hundreds of times smaller than the Logos, are the first to be short-circuited by the electrical storm in the clouds. Soon after, it short-circuits the Logos, but momentum carries the Logos just over the clouds. We know the ship is short-circuited at that point, not only because it seems to coast above the clouds (flying in an arch as if it had been thrown above the clouds), but also because Trinity is forced to "restart" the ship on their way down just before crashing.
First, we must realize that one of the traits that Neo absolutely must have that allows him to be the One is the ability to perceive small time intervals like no other human. Trinity points out that Neo can "move like them", referring to Neo's resemblance to Agents dodging bullets. For more support of this, see Neo: The Machine. From Neo's perspective, he experiences time as if it were moving in slow motion, just as we see him dodge bullets in slow motion. Neo's reactions and thought processes are clearly far above human standards.
This perception of small time intervals is part of what gives Neo the ability to assimilate and process programs that are meant to be run by a computer system. When the Architect alters Neo's consciousness, he's probably incorporating a communication protocol into Neo's consciousness so that the Architect can communicate with Neo in his own little virtual reality. This communication protocol would presumably be rejected by anyone but Neo, which is probably one of possibly many reasons why only the One can enter the Source. Nobody else could handle the necessary alterations. Naturally, this communication protocol stayed with Neo as he left the Source.
As for the transmission of the communication, most assume that Neo's headplug is responsible for broadcasting wirelessly between Neo and the Source. However, this doesn't reconcile with the fact that Neo seems to be immune to EMPs despite his headplug being active. For background on this point (to understand exactly how EMPs work with humans' headplugs), be sure to read Smith: Bane-Smith and pay special attention to the section "Bane-Smith's Coma." After that, consider the fact that Neo's headplug seems to be active all the time; it’s not just active when he stops the sentinels with his mind or when he gets trapped in Mobil Avenue. In the end of M2, he says, “Something’s different. I can feel them.” Was he actively using his headplug at that point? The feeling seems to have come to him, not the other way around. How can he detect the “feeling” of the sentinels in the first place if his headplug wasn’t at least “listening” for them at some level, and therefore active?
If the headplug really were how Neo communicates to the Source, we'd also have to believe that machines implemented some sophisticated strategy of making it so all humans’ headplugs are affected by EMPs when wirelessly active (including Bane-Smith) except for Neo, who has a special EMP-immune headplug with secondary (and undetectable) transmitting powers outside of normal electrical requirements. Does this complicated explanation really fit better than the simple notion of telepathy, which is already undetectable by human technology and, being biologically based, already immune to EMPs? There is also a scene in The Second Renaissance in which machines are testing humans and learning everything they can about humans – they appear to have systematically gone through every neuron of the entire human brain and learn what it does. Until humans are willing to subject themselves to lab testing (not going to happen), they will never learn what the machines know about telepathy.
I also don’t believe that machines have advanced to a point where they have learned how to evade the EMP. If they have, then the vulnerability of sentinels to EMPs would have been a charade in the movies. What’s more, when the sentinels were finally digging, seeking to eradicate Zion and start the Matrix over again, there would have been no reason to keep the “we machines are disabled by EMPs” charade going anyway. Power flowing through metal is power flowing through metal any way it’s spun? Electricity seems to still be the type of “power” that machines run on.
The idea that part of that unused brain could be dedicated to telepathy is a pretty common idea seen in many science fiction movies, from mind readers in Starship Troopers to Xavier in X-Men. This seems the most plausible explanation, considering the beginning of M3:
Maggie: His [Neo’s] neural patterns don’t read like someone who’s in a coma. The strange thing is that I see these patterns all the time.
Maggie: On someone jacked in.
Maggie was monitoring everything about Neo while he was in the coma, and there was no detection of any headplug activity – only brainwave patterns that behaved like he was in the Matrix. This would suggest that machines are tapping into the human brain's potential rather than installing undetectable wireless technology into the headplug of the One.
Because telepathy is a biological advancement rather than a technological one, some tend to resist telepathy as a valid device in science fiction. But telepathy simply treats the brain as a new frontier, just like unexplored space (Star Trek) or unexplored ocean (The Abyss).
With this in mind, Neo's ability to connect to the Source is nothing more than the logical implication of a) perception of small time intervals (allowing for a communication protocol to be "installed" into Neo's consciousness) combined with b) telepathy as a path for this protocol to take place. For more on this theory, see Oracle: The Believer.
There seems to be two stages in the progression of Neo's communication abilities with the machines. At the end of M1, we see that Neo can already sense the machines. We hear Neo say to the machines through the phone, "I can feel you now," just as the computer screen reads, "WARNING: carrier anomaly". Although Neo can "feel" them, he cannot communicate with them yet because 1) he has not yet been granted certain privileged access levels to the Source that would allow him to destroy sentinels, and 2) no communication protocol has been given to Neo enabling the connection. He has only been made subconsciously aware of the telepathic connection to the Source.
The most obvious support for the idea that Neo's communication development went in stages comes from the quote above ("Something's different. I can feel them." - Neo, M2). Even though Neo could already feel them at the end of M1, apparently he could really feel them at the end of M2, or he wouldn't have said "Something's different".
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