Most people who watch the three movies conclude that the Oracle's prophecy was false, but believe it or not, every part of the prophecy came true. In M1, Morpheus told Neo the Oracle's prophecy:
Morpheus: When the Matrix was first built there was a man born inside that had the ability to change what he wanted, to remake the Matrix as he saw fit. It was this man who freed the first of us and taught us the truth. When he died, the Oracle prophesied his return and envisioned that his coming would hail the destruction of the Matrix and the war, bring freedom to our people."
First, regarding the past, all Morpheus was told about was the previous cycle of the Matrix. Little does Morpheus know, this "man born inside" was simply the previous One fulfilling the last of his duties to the cycle. The Architect tells Neo that the function of the One is to return to the Source and then select 23 people to free from the Matrix and help build the next Zion (for more on this, see Matrix System: The One). When Morpheus speaks of "the first of us", he is unkowingly referring to the original 23 people that were freed from the Matrix to form the current Zion. Since that was 100 years ago, Morpheus did not witness this happening firsthand - the story would have been documented and passed down three or four generations before Morpheus would be born.
Regarding the future, here are the four points of the Oracle's prophecy that most people think were not fulfilled, with explanations of how they were actually fulfilled:
At first it appears Neo wasn't the One, even at the very end of M3 when Neo fights Smith, because although Neo can stop bullets and make knives fly into his hands, he could not snap his fingers and make buildings turn into cats. However, consider the fact that Neo's consciousness is altered after he sees the Architect (after that, Neo can actually communicate with the Source), and that his code is again shown to be different when he exits Mobil Ave. (Link does not recognize Neo's code). It's very easy to assume that the One's code would be altered in the ultimate way once the One chooses the right door, as the previous five Ones all did. The One is likely made into a Matrix God, able to control anything he wishes, because this would make it even easier for the One to convince 23 people that the world they are living in is a lie.
This didn't happen, since Neo actually chose the left door. But that doesn't matter to the prophecy. Whether Neo has been granted full access to remake the Matrix as he sees fit yet or not, he still represents the return of the One who was able to remake the Matrix.
Hail in this context means “call forth” or “summon”, and the word "hail" was used with extreme deliberance. Because of that one word, the prophecy does not imply that destruction will actually happen - only that it threatens to happen. By killing Agent Smith in M1, Neo indirectly hailed (called forth) the Smith virus, which threatened destruction of the Matrix. The Oracle simply left out the irony that Neo would also be the one to prevent the destruction of the Matrix.
There is no easy way to actually destroy the Matrix, since billions of people would be left without a place to go. Zion is nowhere near large enough to accomodate that many people that quickly, and the Earth has no animal or plant life to survive on. Billions would die.
What Neo achieved is not just a truce, it is actual peace. No peace between anyone is necessarily everlasting. If that peace is broken, it will be the beginning of a new war, not a continuation of the old one for old reasons. This is not a cease fire that necessitates resuming, it is a peace that will last “as long as it can”, just like any other peace in the world.
First, if Morpheus is quoting the Oracle in exact words (which he likely is since nobody respects the Oracle's words more than Morpheus), then the phrase "our people" may simply refer to the people of Zion since the people of Zion (redpills) are independent from the people inside the Matrix (bluepills). That means this part of the prophecy does not predict freedom for people inside the Matrix. It just means that redpills will be able to jack into the Matrix without being hunted by Agents, and it means hovercrafts can fly in safe zones without worrying about Sentinels - in other words, Zion will be broken free of the Matrix cycles of destruction and creation.
Even if the prophecy is applied to people inside of the Matrix, it does not say that Neo will bring "total freedom" to people, but rather just "freedom". Did the U.S. Civil War instantly bring "total freedom" to blacks, getting rid of all segregation and discrimination and allowing them to attend the best colleges and get the best jobs, or did the Civil War just bring "freedom" to blacks? Remember, this prophecy is laid out by a machine and must not be interpreted as any more or any less than it actually says.
Having said that, Neo still brought very significant freedom to humans in the Matrix. Everyone who wants out of the Matrix will get out, and everyone who is freed from the Matrix will be guaranteed to live. To better understand just how significant this new freedom is, see Neo: What Neo Changes. Also, is the Matrix really that bad if people are all allowed to escape if they choose to reject their world?
Morpheus and Neo had no way of knowing at the time of their conversation that Neo would be revisiting the Source through a different route, directly from Machine City. The war did not end after Neo originally returned to the Source through the white hallways. Morpheus was shattered when Neo told him that the prophecy was a lie and just another system of control. However, it turns out that both of Neo's conclusions were flat out wrong. The prophecy turned out to be true, and every bit of guidance she gave to people was aimed at breaking the primary cycle of control (the cycle of the One creating Zion, then Zion training the next One). So, the Oracle's prophecies and guidance to each person were not part of that system of control at all.
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