Wouldn't the anomaly only have been created after there were too many freed humans? If that wasn't the purpose of the first anomaly then what was it? Or if it wasn't the first anomaly who freed all the first humans then who was it?
None of the works in the franchise (movies, comics, video games, etc.) explain how the first anomaly (and the humans who built the first Zion) escaped the Matrix, as far as I'm aware. I can think of two ways in which the first anomaly may have escaped the Matrix:
- Self-substantiation (just as Kid from the films, Dan Davis from The Animatrix, etc.). The problem with this is that it would be very difficult for the first human(s) who self-substantiated to survive outside of the Matrix without any pre-existing support from a human settlement such as Zion.
- The machines willingly released the first anomaly (perhaps with other humans who were starting to reject the Matrix) and gave them some initial support so they could survive and found the first Zion.
To understand why the machines might release the first anomaly, we must explain what the anomaly is and what the machines are doing about it.
The anomaly is not an entity that was purposefully designed by the machines; instead, the Architect describes the anomaly to Neo (who is the sixth integral anomaly) as:
Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the Matrix. You are the eventuality of an anomaly, which, despite my sincerest efforts, I have been unable to eliminate from what is otherwise a harmony of mathematical precision. While it remains a burden assiduously avoided, it is not unexpected, and thus not beyond a measure of control... As you are undoubtedly gathering, the anomaly is systemic – creating fluctuations in even the most simplistic equations.
The Matrix Reloaded (transcript)
The anomaly is a systemic error, a nuisance that the machines cannot get rid of despite the Architect's best efforts. Furthermore, this error grows over time, which is why Neo and his predecessors are "integral" anomalies ("integral" because they are "sums"). What is important to note is that the anomaly exists whether or not any humans have escaped the Matrix -- it is an inherent flaw in the Matrix. The Oracle managed to find a solution where 99% of humans would accept the Matrix, but she could not eliminate the anomaly. The 1% of humans who "refused the program"
while a minority, if unchecked, would constitute an escalating probability of disaster.
The Matrix Reloaded (transcript)
However, the machines devised a clever way to obtain some "measure of control" over the anomaly: they allowed the creation of Zion for the minority who rejected the Matrix, and they designed the One, whose purpose is described by the Architect as follows:
The function of the One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program. After which, you will be required to select from the Matrix 23 individuals – 16 female, 7 male – to rebuild Zion. Failure to comply with this process will result in a cataclysmic system crash, killing everyone connected to the Matrix, which, coupled with the extermination of Zion, will ultimately result in the extinction of the entire human race... [T]he relevant issue is whether or not you are ready to accept the responsibility of the death of every human being on this world... Your 5 predecessors were, by design, based on a similar predication – a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of the One. While the others experienced this in a very general way, your experience is far more specific – vis a vis love.
The Matrix Reloaded (transcript)
In other words, the machines designed the One to both integrate/sum the errors/rejection of the Matrix (hence Neo and his predecessors are "integral" anomalies) and experience an especially "profound attachment" to humanity. This allows the machines to blackmail a single person (the One, and integral anomaly) into willingly rebooting the Matrix (resetting the errors/anomaly to zero for the next iteration) in order to avoid the extinction of humanity. At the same time, the machines can "reset" Zion in the real world (which they could do without the One, of course, except that the destruction of Zion is the threat to the entire species with which the One is blackmailed).
What all this means is that the machines figured out how to handle the unavoidable anomaly (which is inherent to the Matrix and thus exists whether or not any humans have escaped the Matrix) by (a) allowing those who reject the Matrix to build a human city in the real world (Zion), and (b) designing a program of sorts (the One) to sum the humans' rejection of the Matrix (as the "integral anomaly") and periodically re-stabilize the Matrix. The One is also a human who rejects the Matrix (more than any other human, in fact), so the machines want/need him or her to "escape" from the Matrix to Zion. Therefore it is quite likely that the machines willingly released the first anomaly and perhaps other humans to build the first Zion.
I think you're thinking of the Anomaly as a function of the Machines trying to control the humans. The problem with that theory is that The Architect indicates they can neither control, nor stop, the Anomaly (quotes from this transcript, all emphasis mine)
The function of the One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program. After which, you will be required to select from the Matrix 23 individuals – 16 female, 7 male – to rebuild Zion. Failure to comply with this process will result in a cataclysmic system crash, killing everyone connected to the Matrix, which, coupled with the extermination of Zion, will ultimately result in the extinction of the entire human race.
The Anomaly is only described as
Architect: The first Matrix I designed was quite naturally perfect, it was a work of art – flawless, sublime. A triumph equalled 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.
Neo: The Oracle.
Architect: Please. 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 probablility of disaster.
From this we can surmise something: the original One was inevitable, based upon how The Matrix works. Thus, it's not unrealistic to assume that this "original" came about the same way Neo did: they willed it. They made choices that ignored the limits of The Matrix and they started to break it (the Anomaly). We never see Neo free people by force of will (in fact, we never see him free anyone in a direct fashion). So, my speculation is the sequence was something like
- Zion is established after the war with the machines ends
- The Original One appears, bringing with them The Anomaly
- Somehow, The Original makes contact with Zion and plots to overthrow the Machines. It's not clear if they could free humans directly, but clearly other humans figure that part out (as we see Morpheus free Neo, Trinity, etc)
- The Architect, having realized what would eventually happen, plans The Reset and The One finds their way to him
- The same threat is made as the one to Neo: we wipe out Zion, you repopulate it with folks you pick from The Matrix and we kill you (disseminate code) which stops The Anomaly and we all start over. Or everyone dies. Your choice.
- Clearly, The Original picks door #1 and resets, thus saving humanity. Everyone in Zion who knew the truth is killed and replaced with a small band of Matrix folks who start to procreate. And thus we have what Morpheus tells Neo: they were freed by The One and The Oracle prophecies the One will come again, so they all start looking for the next One. And thus the cycle is born.