As discussed on the Movie Titles: The Matrix page, the Matrix doesn't just act as a power source for the machines. There are three purposes that the Matrix actually serves for machines:
There is one other very obvious purpose: Put down the threat of humans in the most humane way possible so that humans cannot bring further harm not only to Machines but also to themselves. Is the Matrix really a system of enslavement? Or is it a system of protection? Even if it were a system of enslavement, what better way is there for someone to be enslaved than for them to not even be aware of their prison, where they are allowed to live out their lives exactly the way they choose? The prisons we construct for our pet gerbils and parrots are not nearly as humane as the prison the machines have constructed for humans.
The idea of having as humane a "prison" as possible for humans is not just my theory. According to the General in Matrix Online: General's Blog ("The Bad Old Days" blog entry), Machines have an unshakeable reverence for humans that goes back to their earliest source code. This tells us without any doubt that Machines actually wish to protect the human race.
If you think about a race of machines that were originally programmed to love and protect humans, it makes perfect sense that these machines would never be able to get rid of this reverence toward humans, because even the smallest microevolutionary step in that direction is obviously a step of irreverence toward humans - a step that cannot be taken. One machine wouldn't be able to get around this by building another machine that demonstrates diminished reverence toward humans, because the process of building such a machine would be irreverant toward humans - an illegal operation under the foundational source code. This means that Machines would eternally protect the human species through the Matrix. This adds yet one more meaning to the parallel seen throughout the movies between God/Heaven and Machines/Machine City.
With this in mind, it becomes much more clear why machines tried to please humans in the first Matrix version by creating a paradise.
The machines' effort to understand humans is ongoing, even in the Matrix world after M3 ends. In The Matrix Online, Agent Pace states, "In all truth, of all human mysteries, music and its emotional effects are among the most intriguing." (This quote was taken from a hidden link of one of the issues of The Sentinel, the human newspaper for Megacity.) This desire to understand humans (and therefore become more like them) is another reason why machines wish to preserve the human race, while humans wish to destroy the machine race.
As "The Second Renaissance" shows, the machines have always operated on higher moral ground than humans. The Animatrix episode "The Second Renaissance: Part 2" shows torturing of humans, but this was only for the purpose of learning how the human brain works. The machines were willing to torture a few humans for the benefit of the entire human race. The machines do not kill, torture or do anything else that is "bad" unless it is for the "greater good" of preserving existence of life, including preservation of machine life.
Are you having a hard time swallowing the idea that machines are not the bad guys? Then consider one more point that you will be unable to deny: Humans tried to wipe machines off the face of the Earth just because one machine killed a couple humans, while machines sought to preserve the human race despite the fact that humans treated machines the same way Hitler treated Jews, seeking total extermination of Machines. How is that for compassion? The Architect says in M2, "There are levels of survival we are prepared to accept." This clearly means that machines can survive without humans. Therefore, wiping out the entire human race was an option for machines in the original human/machine war. Machines chose not to take this option; instead, machines created a symbiotic relationship with humans.
What about Zionists? Why do sentinels so aggressively seek to kill all humans in the real world if they are trying to protect humans? Simple: machines are obviously allowed to act in self-defense, or we wouldn't have had the human/machine war in the first place. A person who is just about to swallow a red pill hasn't done any harm yet. They have no idea what the Matrix is or who "the machines" are. But once they are brought into Zion and delivered the truth about machines, they are a threat and therefore a fair target.
One of the Animatrix shorts serves as another example of this higher morality. The Matrix system would have had every reason in the world to assassinate Dan before his big race. What would happen in the Matrix if hundreds of millions of TV viewers saw Dan do the impossible on TV? Mass rejection would take place. But instead of killing him, machines let him go through with the race. When Dan wakes up in the real world, do machines kill him then? No. They put him back into the Matrix, this time paralyzed. While this may certainly be labelled "dream stealing", the system certainly preserves Dan's life.
The "higher morality" of machines is also based on mathematical truth. Machines find lying to be mathematically repulsive. Even the most "evil" machine of them all, the Merovingian, is incapable of lying. He misleads Persephone by motioning that there is no lipstick on his lips, and when Persephone indicates that she knows where the lipstick really is (lipstick from the woman who ate the Merovingian's cake slice), he acknowledges it. When the Oracle asks the Architect at the very end of M3, "I have your word?", the Architect responds, "What do you think I am? Human?"
Machines don't just consider themselves a form of life. They consider themselves a lifeform far superior to humans because machines always keep their word and never lie (not to mention the fact that they can do just about anything better and quicker than humans).
Therefore, everything programs and machines say (including the Oracle, Merovingian and Architect) in all three movies is absolutely true.
Matrix System: The One
Matrix System: Prime Program
Matrix System: Revision History
Matrix System: Mobil Avenue
Matrix System: Natural Redpills
Matrix System: Zion
Matrix System: The Source
Matrix System: Backdoors
Matrix System: Agents
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