Something that all you matrix fans might find interesting.
Here we go with the basics.
Zion is real! The Matrix is not.
The Matrix was designed to provide a mental stimulus for the human bodies connected to the machines as a source of power. This is the sixth version of the Matrix. There have been multiple versions of the Matrix because of a flaw in the program (kinda of like Windows). That flaw is giving individuals the ability to choose.
The first Matrix was designed as a perfect uptopia (see pt. I – Smith explains it to Morpheus; pt. II – The Architect explains it again) but humans did not accept it as real so they just kept waking up. It was redesigned to reflect our civilization at it’s last stage before it was taken over by the machines (the year 1999).
The Architect’s problem with this new design (the anomoly)of the Matrix is that it require individuals to think freely, i.e. choice. It was the Oracle that suggested he redesign the Matrix in this way. But since humans have choices, so must the programs sent to watch over them, i.e. The Agents, thus bringing us the problem that is Mr. Smith. In Reloaded, The Architect continues to speak of the anomoly he is unable to get rid of, which is why at some point, he feels the only solution is to destroy the Matrix and those who are aware of it (the people of Zion) and start from scratch again.
The Oracle says it clearly in Revolutions. Mr. Smith is the result of the anomoly trying to balance itself. Mr. Smith began to think freely (see part I where he is freaking out while interrogating Morpheous) and the result was a negative one. Realize this, he is a similar program to the One so he is far more dangerous than a normal individual who makes bad decisions. Mr. Smith’s virus like behavior happened in EVERY VERSION OF THE MATRIX. The result would always lead to the same thing — a system crash if they didn’t quickly reboot the system. The same knee jerk reaction you have when you realize someone has sent you a virus.
The One program was created to solve this problem. But each version of the One ultimately failed. Neo is different, in Reloaded he choose the door that led to Trinity, not the door that RESETS the program. Note: The Architect even noticed that Neo’s experience in the Matrix was different than all the rest, realizing he was the first of them to fall in love.
Neo’s choice has changed everything. The system is still threatened by Smith’s behavior, so the Oracle makes a new choice; one she has never done before because no version of the One has ever chosen the difficult path as opposed to easy one of just resetting the system. She allows herself to become merged with Smith in the HOPE that she’ll be able to help Neo when the time is right.
Neo makes another unique choice. He goes to the machines and asks for PEACE as opposed to simply destroying the system by going through the opposite door as all other versions of the One did. It was a simple as that to save Zion. Machines don’t need very long to process that this may be a better idea than just constantly resetting the system.
At the end, Smith says to Neo the movies tagline – “Everything that has a beginning has an end,” as the Oracle is speaking to Neo through Smith. Neo realizes it all along, the only way to end this is to sacrifice himself. The Oracle noted that Neo and the Source (the computer mainframe, the Architect they’re all one and the same so don’t get confused) are connected which is why he can control machines outside the Matrix. He uses this connection to his advantage. He becomes a Mr. Smith and since all the Smith’s are connected, the Source now has a lock on Smith and simply deletes him. Pretty simple huh?
For those that like to dig deeper, than note the biblical references throughout the series. Heck, the French Man (Merovigchian) is the Devil, just read the elevator button Morpheous presses when he goes to see him for the second time. The Architect represents God – i.e. the creator of the world and its destroyer whenever things don’t go as he wants. He even has you to chose a select group of people to restart Zion again sort of like Noah’s Ark. Neo is Jesus, the one who realizes that peace and love is the answer, not war and also sacrifices his life so that others can live. And the Oracle represents the Holy Spirit. This of course is secular but none the less very deep and spiritual. It’s a deep trilogy if you PAY ATTENTION.