The first Matrix I designed was quite naturally perfect, it was a work of art-flawless, sublime. A triumph equaled only by its monumental failure. The inevitability of its doom is apparent to me now as a consequence of the imperfection inherent in every human being. Thus, I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus the answer was stumbled upon by another - an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother....As I was saying, she stumbled upon a solution whereby nearly 99% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level. While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo those that refused the program, while a minority, if unchecked, would constitute an escalating probability of disaster.

The Matrix is a system, Neo. That system is our enemy. But when you're inside, you look around. What do you see. Business men, teachers, lawyers, carpenters. The very minds of the people we are trying to save. But until we do, these people are still a part of that system....You have to understand that most of these people are not ready to be unplugged and many of them are so inured, so hopelessly dependent on that system that they will fight to protect it.