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there's a realization that makes the first Matrix so interesting. In-universe, Neo is not important, like, at all. Until he becomes the one. People might miss this, because he's the main character. But he's not important yet.

The WHOLE movie, Morpheus is the target. Not Neo. (Which is why it was kinda dumb that Morpheus sacrificed himself to save Neo, because he was the one they wanted anyway. Anyone else could've done it. But he didn't know that so it's okay.)

The only reason the Agents bother Neo is because he has had contact with Morpheus via Trinity. So they put the tracker in him, so if Morpheus finds him again, they can track him. Now, the only window to do this is when Neo is in the pick-up car. If an Agent takes over Neo's body before that, then they can just not pick him up. So they have to take over Neo's body when he's already in the company of Morpheus. But when they get him in the car, Switch points a gun straight at him. So can't take over his body then. Then they drop the tracker out of the car.

As for why they don't take him over when he's in the room, I think the room is kind of a special hack that makes it untraceable. It's the same room that the team discusses their plan in in Reloaded. After that, he was redpilled so he's good to go.

An alternative theory is that Agents can only take over the 99% who unconsciously choose to accept the Matrix. Since Neo rebelled, his mind couldn't be controlled. Makes sense since the Agents are literally the system, and the 1% reject the system.

This requires watching Reloaded though, and also assumes that Reloaded was planned from the beginning. So I think the first explanation is better if you're just taking The Matrix as a standalone film. But in the context of the entire story, both explanations can be true.

I like the second theory more, cause the agents should have been following the dude a lot more tbh.

Thanks for this btw!

They didn't know he was related to Morpheus until the night before his release though. We see everything Neo does after he gets the attention of the Agents.

They knew trinity was targeting him "We know their next target, his name is neo" tho. So they had to assume morpheus thought he was important, even though he was beyond the normal age of somebody being freed from the system.

also the bug was meant to be subtle. If they were following Neo around, Morpheus still wouldn't have him picked up.

the only reason they got caught is because Trinity saw Neo get taken by Agents. so she assumed they bugged him

if they took over Neo then it'd be pointless. Morpheus would just forget about him. they had to track Neo

another plot point xd. Why didn't the agents turn around when arresting him.

Smith does notice Trinity though. But what were they gonna do? Not bug him? lol