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According to the Architect, the emergence of the One is predictable and inevitable, it has already happened 5 times before, and the current iteration turned out to be Neo

If it is inevitable, when does the Matrix system know who or where exactly is the One? It doesn't seem possible for just anyone to become the One. Does that mean the One gets marked from birth that he is, in fact, "The One", or does he have to discover himself as "The One" for the Matrix to realize that it's him?

What I mean is, if the coming of the One is inevitable, and there can be only One, then why didn't the agents or Morpheus track down Neo when he was a baby? When does whatever sign that it is, which alerts the agents or Morpheus of Neo being the One, start showing itself?

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The short answer to your question is that the Agents have been tracking him for quite some time, along with various other "potentials" but they're not mandated to tackle redpills unless there's a compelling reason to do so. In-Matrix, the police can deal with low level hacking and nuisance.

Once he comes to the Agent's attention, it becomes apparent that Neo has a bulky file (complete with tracking photos and a scan of his passport) but it's not until Morpheus makes contact with Neo that the Agents start to show more than a passing interest in him. Had they known that he was "the one", Morpheus suggests that they would have simply killed him from the word 'go'.

Morpheus: This line is tapped, so I must be brief. They got to you first, but they've underestimated how important you are. If they knew what I know, you'd probably be dead.

Neo: What are you talking about. What...what is happening to me?

Morpheus: You are the one, Neo. You see you may have spent the last few years looking for me, but I've spent my entire life looking for you. Now do you still want to meet?

The sign that Neo is "the one" is pretty vague. An earlier version of the script suggests that Morpheus is actually a bit of a kook and that he's tagged other people as potential 'ones' in the past, all of whom have died while trying to confront Agents.

CYPHER : I'm going to let you in on a little secret here. Now don't tell him I told you this, but this ain't the first time Morpheus thought he found the One.

NEO : Really?

CYPHER : You bet your ass. It keeps him going. Maybe it keeps all of us going.

NEO : How many were there?

CYPHER : Five. Since I've been here.

NEO : What happened to them?

CYPHER : Dead. All dead.

NEO : How?

CYPHER : Honestly? Morpheus. He got them all amped up believing in bullshit. I watched each of them take on an agent and I watched each of them die.Little piece of advice: you see an agent, you do what we do; run. Run your ass off.

Morpheus does speak to how he knew where to look for Neo, the answer being that he spotted him in a chatroom and felt certain urges...

MORPHEUS : And then I saw you, on the Net, searching for me and everything changed. I felt this charge, this electricity through my whole body. I started laughing and tears poured out of my eyes, because I knew, I knew that you were the One.

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    While this answer is correct, Morpheus is likely wrong that they would have killed the One. Remember, the prophesy Morpheus believes in is a ruse created by the Oracle. They wanted him to get out, go through a trial, and wind up at the Architect, where they expected him to choose to sacrifice himself. We can however infer they didn't know he was the One, or else the Agents wouldn't have killed him. Plus, based on what the Oracle said, he didn't actually become the One until his next life, when he came back. – trlkly Aug 5 '14 at 8:13

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