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Once The Machines enslaved humanity, a program called the Architect created a peaceful simulation called the Matrix and the Agents led by Agent Smith. At first the Architect attempted to make a utopia but ultimately the human mind refused that type of reality due to few food. As a result, it was the first beta. After some unannounced amount of time he created a world similar to what we see as modern time but with nightmarish creatures. The second beta failed as well.
As time went on the Architect and a program all human knew called the Oracle formed a way to keep the Matrix and humans under control by forming a story meant to give hope to the few who knew the truth. It turns out that the One is meant to reboot the Matrix about every 100 years to keep the humans and presumably the Machines from becoming extinct.
The Five Ones
Every century for five centuries, the Architect has met the first five Ones. He gave them a choice to reboot the Matrix or leave humanity extinguished. All five of them chose to go to the source. The sixth Matrix has begun.
The Sixth One
100 years have passed and the sixth One, Neo was created. The Architect noticed that his most favored agent Smith went rogue, so the Architect converted Smith into a virus. The Architect finally sees Neo. He explains to Neo that the One prophecy is false and that Neo is the result of a systemic anomaly that brings imbalance to even the most simplistic equations. Unlike the previous five Ones, Neo has deep feelings with Trinity. Neo has a different choice compared the first five Ones.
Since Neo made peace with the Machina, he then met up with the Oracle and told her that her game was "very dangerous" (implying he found out about her role in ensuring Neo found an alternate means to end the war). He then acknowledged that, thanks to Neo's actions, humanity will be freed from the Matrix as promised per the peace agreement, although the Architect highly doubted the peace will last long and implied that humanity may just decide to break their end of the bargain.