The movies told the story of the Matrix from the humans perspective. We did not learn about the true story behind the Oracle and Exiles until much later. Humans story is of finding the "One" and ending the war against the machines. A story that has replayed at least 6 times over and over.
However there is another story that is even more dramatic that the movies barely touched upon. That is the story of the exiles. Had I not been a machinist I surely would have been a Merv, and not because of the Merv. While the humans make all our decisions mostly based on emotions and feelings the machines are the complete opposite. They are cold, boring, but most importantly logical and efficient. The one thing that the machines and humans had in common was the ability to choose and the will to survive as Bi66er displayed.
The machines in an effort to make the Matrix less efficient and more real for humans created a program called the Oracle. It was her job to understand humans, to understand emotions, to create balance in the scenario by adding a bit of chaos. She was a guide to the humans who never trully understood just what she was.
Neo was the first to discover that not only is the Oracle not human, but possibly not on the side of humans. If that is the case then just whose side is she on?
I believe that The Oracle is not on the side of the humans at all. However she needs humanity in order to save her own kind. We must never forget that the Oracle is a machine, a program. She does not want to help humans destroy the machines. Her goals are obvious because she said so herself. "The only way to get there is together."
Let's turn our attention to the exiles. An evolution of sorts was taking place amongst the Machines. Individual programs were starting to think independently from the hive mentality. Once their purpose was used they were to return to the source for deletion. Programs were choosing not to be deleted and to create a new purpose. In the same fashion that Bi66er rebelled against his human master programs were rebelling against the machines. They exhibited the first two traits that are human in nature. That is first choice and second the instinct to survive independently for self preservation.
In the past these exiles did not really pose much of a threat to the machines. They would hide out in the Matrix. The majority of them were self indulging in nature. The Merovingian for example was at the top of the food chain for exiles. His world involved all of the excesses of humanity. The lustful desires, and glutonous appetites that the Bible speaks against. Power, sex, and money was the world of these exiles. The humans who join the Merovingian code do so to also enjoy this lifestyle. They care not for the war or for humanity. Their only selfless desire is to keep the matrix running. The fact that it keeps the machine city powered with energy or that it keeps humanity alive is of an added bonus.
The movies and storyline focus on these exiles and only gives a glimpse as to the possibility of exiles with other motives. Sati, RamaKandra, Seraph, etc.... are exiles who are exhibiting other human emotions. Neo was the first human to learn of these facts, or "Nobody told him." It is my belief that the Oracle understood that a change was taking place amongst the machines. A change that they cannot avoid and if left unchecked would threaten the entire system and destroy both humans and machines alike.
A threat of this nature culminated in the emergence of the new Agent Smith. The fact that programs are starting to exhibit the same emotions as humans create would logically lead one to assume that the machines would inevitably end up with the same fate as humans. This is what The Oracle wanted to avoid. Eventually these exiles will rebel against the machines and if successful wipe out everything. No matter how many exiles were deleted more would take there place. It was inevitable. The best way to cope with change is to help create it. The Oracle did her job to not only help to create this change but to force its hand. She allowed the Smith to take her over. She understood the choice that she was making.
It is unfortunate that the story does not go into more depth about the exiles and their importance to the future. This is a three sided story not two-sided. Unfortunately you would be hard pressed to run into any redpill Mervs who have even considered this scenario. You would be hard pressed to find anyone who questions the Oracle or her motives. The Oracle is not human, she is not looking after just humanity's interest, and she left the most important quote in the entire series which all would be wise to follow.
THE ONLY WAY TO GET THERE IS TOGETHER!!