The Matrix Reloaded - Groked.

I groked matrix reloaded and now got it.

Forget all the philosophy in the movie and the double meanings of names. Think of the matrix and machines in terms of software and rule based algorithms.
I believe, like Morpheus is so fond of saying, that the matrix built by the machines is just a complex adventure game, or Multi User Dimension or MUD.

The first Matrix as told by agent Smith was a perfect world where everyone was happy, everything was right, everything was simple, basically a pointless MUD game, therefore a game you can finish very quickly and gets boring very quickly also. Imagine if that boring easy game was your life and you quickly mastered it? You would lose purpose, hope, and happiness. Everything would be boring and pointless; you probably would get depressed and go insane. That is exactly what happened in the 1st matrix version made by the machines.

The new matrix, or could I say matrices, where more developed and morsuitablele for struggling humans, you had the illusion of difficulty, the struggle to succeed, the struggle to merely survive, a regular hard life which is what everyone in the matrix is experiencing. Now the story of the first matrix was the story of hackers who began to realize that they where living in a MUD/ Matrix, got out of the matrix and mastered the game since they where able to analyze and comprehend the matrix at a very low level.
Neo, the one showed potential to understand the matrix at an extremely low level even bypassing the rules of the game / software / matrix and being able to for instance stop bullets, flying likSupermanan and destroying agents. The MUD/Matrix was not designed for that.

In the Matrix I we are shown the Matrix as the real world and then it is revealed that it is not a real world but a very good simulation. Morpheus and Trinity are still playing by the rules of the game but with great skill, Neo is told that he is the One, meaning the best game player around. Neo starts understanding or believing his skills and doing what was previously thought to be impossible.
In Matrix Reloaded, we see the different game stages, with characters of the Matrix telling them what to do next. As in any MUD, the simulation is good but not good enough to cover all events so you have to guide the players through clues.

Try to think like software and you will understand how the matrix behaves, causality is simply and if - then statement, or a case statement.

Neo is the only One who showed independent thought, blinded by his love for Trinity, to take the door sending him back to the matrix. With that result Neo became the controller of the matrix and managed to stop the probes while he was in the real world. Neo somehow mastered the game and ended up controlling it.