Neo's Powers: Stop Sentinels

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:

• After Neo enters the Architect's room and is again in the real world, he somehow knows that the strange machine on their scanner is going to send a bomb their way. Nobody else was able to figure this out since they've never encountered such a machine before, but Neo knew exactly what was happening even before the machine started spinning the bomb.
• At the end of M2, Neo says, "Something's different. I can feel them."
• At the beginning of M3, we learn that Neo's mind was separated from his body. This would be absolutely impossible without some kind of connection between Neo and the Source.

These clues are confirmed when Neo speaks to the Oracle in the third movie:

Neo did not need to physically shock or EMP the sentinels to destroy them - he only needed to communicate with them through the Source.

Countermeasures

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. So, when Neo used his connection to the Source to destroy sentinels (something Neo is given permission to do with the assumption he'll choose the right door), the system implemented a countermeasure to make sure he couldn't do it again. We see this countermeasure in action in M3, the second time Neo tries to destroy sentinels. The sentinel fights back by appearing to fly through Neo in a virtual reality world. Neo appears shaken quite a bit from it. The sentinel is probably messing with Neo’s mind just as Neo’s mind can affect sentinels through the Source.

However, right after that countermeasure is carried out, Neo immediately senses that going into the clouds will destroy the sentinels, probably because the rule is part of the sentinels’ programming. In M2, Neo similarly knew that the sentinel was going to hurl a bomb toward the Nebuchadnezzar before the machine even began the twirling.

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.

Enabling Factors for Neo's Connection

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 probably 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, it is a fact that we do not use certain parts of our brain (a majority, in fact), and the idea that part of that unused brain could be dedicated to telepathy is a pretty common idea seen in many science fiction movies (for example, the mind readers in Starship Troopers). If we are truly fair to the Wachowski brothers and let them use the telepathy idea without having to explain exactly which neurons are firing inside the brain to make it happen, then 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.

Two Stages of Neo's Communication Development

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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