Some people look at a movie and see it as just that: A movie, nothing more, and nothing less and no deeper than a story on a screen. The Matrix is well renowned for its action and cinematography, especially the introduction of "Quicktime." What many fail to recognize is the depth the series really has. Layers. The best way to describe the quality of this story is with layers. Those layers are what lie ahead.
Dreams, what are they? And how do you know you"re not in one? A recurring subject in the films is dreams. The "Matrix" is a dream world in every sense of the word. A place beyond reality, yet directly attached to. The only thing that tells us that we have dreamt at all is waking up with a recollection of organized thoughts. The main character Neo, has lived his whole life in a dream and just now awakes to find it was all a dream. He spent his whole "Dream" thinking he was in reality. Knowing nothing else to be a possible reality, having no idea he was a tool. .
Brain-in-a-vat syndrome. Neo awakens to find that he was not in a dream per se but in an artificial reality. Something created by a superior intelligence to control the beings they [The Machines] were using as energy sources. Some people watching the films left asking themselves "How do I know I am really alive?" A question often resolved by faith, or mere forgetfulness, some people just don't care; we are where we are and know of no way to change it. .
Experience is what it's all about or so some think. There us a factor of the movie that brings about a moral dilemma over doing what is wrong, and doing what is right, and doing what is best for you as an individual, or is best for everyone. Cipher made the choice to do what is best for him. In a scene with Agent Smith, Cipher makes a deal to sabotage the Nebuchadnezzar in exchange for being reinserted into the matrix, with no memories of any of his life in reality. He chooses to be wealthy and comfortable in ignorance, instead of poverty stricken and fighting for every step of the way to freedom.