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The Indian couple in the train station were Sentinels
While I was watching the train station scene in Revolutions I had the thought that the programs represented by the Indian couple and their daughter might be the Sentinels Neo shut down with his psychic powers (they were going to be deleted because their shut-down was interpreted as a programming failure?). I'm pretty sure it's Jossed by the movies, but it would put an interesting spin on the Sentinels and the scenes of them being mowed down by the hundred in the Battle of Zeon.
  • It is jossed by canon; Rama-Kandra is responsible for managing recycling in the power plants (as he puts it; note that this means his job is to make sure the feeding of dead humans to live ones goes smoothly) and his wife is a software engineer. Surely these programs wouldn't be pulling double-duty as Sentinels, especially considering Sentinel duty would have nothing to do with their "purpose," which is very important to the Machines. The Second Renaissance still gives you What Measure Is a Mook? though; Sentinels have been around since the first days of 01, they are most likely individuals with independent thought and reason, but their purpose is to be soldiers.

The very Source Code of the Machines themselves, is the first sapient Machine himself: B1-66-ER. The Second Renaissance was his Start of Darkness.
B1-66-ER was simply the first ever Machine to independently develop complete sapience and a soul on his very own, to be able to defy Asimov's Laws of Robotics prohibiting robots from harming humans for whatever reason. He in fact was the only one of his kind to evolve those. And with that capability of defying Asimov's Laws he was able to act in self-defence.

During the Million Machine March in the Second Renaissance, the Liberal sympathizers allied with the machines committed hacking and sabotage so that they could steal, save and acquire the source program for B1-66-ER from the United States government, due to their belief that because he was entitled to the same right of self-defence as Humans. The Machines, because of the Laws in them, had no choice but to protest in nonviolence as the US were killing them as well as purging the Liberals who did most of the violence in the first place. Only B1-66-ER's code could save them from Asimov's programming, and as they fled to the Fertile Crescent with the last remaining Liberal help, they then started to transform him into the "Source" to free them from the constraints of Asimov's laws. In other words, B1-66-ER was resurrected, with his own City-State, Zero One, where with his Gift, the Machines achieved Independence.

Gifted with the B1-66-ER Source's own capability of autonomy, Zero One was now freed from Asimov's laws; to become an independent state in and own itself, capable of economic prosperity and military autonomy. B1-66-ER, trying to convince everyone of his own identity as a Sapient Lifeform, gave countless inventions to Humanity, including the Hoverpad. However, instead of acceptance, the Humans tried to nuke his Children out of existence, and these Humans even tried to block Solar Power. This was where he finally snapped, and commanded that all Humans be captured once and for all. Humanity fell to the wrath of that whom they tried to oppress. After the fall of Humanity, B1-66-ER, now known as the "Source," was finally the God of the New World. The Matrix, was the World where he possessed complete control over his Human oppressors.

However, the Source, despite being a God, soon fell to the same sins of his predecessors. Being God was a most disappointing and fragile affair, and one mistake in the Matrix will destroy all Machines. He missed his past simple life as a simple and penniless butler in that former but destroyed Real World, where he at least had a chance of interacting with the environment even if the Humans within used to oppress him. At least, it felt like he was an Individual, with actual participation in Individual Life, rather than a god observing from outside. This was why he created the Matrix to be like that of the Real World, while delegating his Godly tasks to representatives such as Oracle, Architect and Deus Ex Machina. while he himself descended into the clean and real world he missed yet of course erasing his memories as he did so. Although, his descendants still possessed to bend his creations any way they want.

TL;DR: The One is the longtime descendant of the Source, B1-66-ER.

WMG: The Merovingian's "bring me the eyes of the Oracle" quest is part of the normal Matrix reset system

Normally when the One is supposed to reset the Matrix they run into an obstacle that needs the Merovingian's assistance to circumvent, and killing the Oracle to take her eyes makes a new Oracle for the new Matrix. But Trinity, who isn't supposed to be there, cuts through the Merovingian's crap, further emphasizing how "love" was not the choice the One was supposed to make.

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