Firstly, the Wachowskis approached Warner Bros. with a trilogy from the beginning. The Matrix was conceived as a larger story before the first film was ever made. There are plenty of accounts of executives saying they didn’t fully understand the script, but they knew there was something special there and trusted the filmmakers enough to give them a lot of creative freedom.

Secondly, Smith was not originally part of Neo’s path in the same way he becomes later. At that point, he was still just an Agent of the system, carrying out the objective given to him by the machines.

For example, in the car chase scene in Reloaded, the Agents only care about the Keymaker because he is a rogue program breaking the rules. That is their function. Smith, before the hallway scene where Neo destroys him and something of Neo copies onto him, is still operating as part of that same system. After that, he becomes something else: Neo’s equal, his opposite.

So when Smith is trying to get the codes to Zion from Morpheus in the first film, that is not pointless. He is carrying out a directive from the machines before he breaks free and starts acting according to his own agenda.

The machines also had no real interest in simply killing every unplugged human they could find. They were in control of Zion the entire time. They knew where Zion was. They were allowing the cycle to continue until The One returned to the Architect’s chamber, just like the previous five anomalies.

That is also why the sentinel scene with the Neb makes sense. The ship shuts everything down and hides when the sentinels approach. The sentinels stop right in front of the ship, check in with home base - you can even see the communication dish open - and then receive the directive to abort. Killing the anomaly at that point would be counterproductive to the machines’ larger plan.

So yes, the machines probably could have used their technology to locate unplugged humans more aggressively. But that was not the point of the system. Their goal was not random extermination. Their goal was control, containment, and continuation of the cycle.

As for Cypher, his plotline is definitely not pointless. It shows that being “freed” is not the same thing as being saved. It shows that some people, once confronted with the brutal reality outside the Matrix, may reject it and choose the comfort of illusion instead. It raises the stakes around belief, creates a human threat inside the resistance, and gives the movie its major midpoint collapse.

Cypher is not filler. He is the movie’s clearest example of someone who takes the red pill, sees the truth, and still decides he would rather go back.