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In the movie, Matrix Reloaded, they say that machines are drilling on top of Zion. In first part, Smith was trying to find location of Zion, he fails.

So how come machines have found location of Zion?

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    Smith wasn't trying to find the location of Zion, he was trying to gain access to Zion via the codes that Morpheus had.
    – Jack B Nimble
    Commented May 17, 2017 at 13:54
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    @JackBNimble .. what does Smith gain from the access codes .. i didn't understand what smith wanted now ..
    – Gomes
    Commented May 22, 2017 at 6:57

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The machines, especially the Architect program, already knew the location of Zion during the events of the movies.

The only reason Zion was allowed to exist because it served a purpose for Matrix. Zion was allowed to exist by the Machines as a giant pressure-release valve on the entire system, allowing the humans who realized the Matrix wasn't real (statistically, only a fraction of 1% of the whole human population) to be conveniently removed and isolated. It should be pointed out that the real threat to the Matrix is not Zion, but the systemic anomaly created by 1% of the population subconsciously rejecting the Matrix.

Once the One is found, trained and sent on the Path of the One to the Architect's chamber, Zion is scheduled for destruction (for a fresh start). When the One reaches the Source to disseminate the integral anomaly, he reinserts the Prime Program, which is the Architect's way of referring to the Path of the One. The Path of the One is a subprogram within the larger programming of the Matrix that ends with the One's arrival at the Source. After disseminating the integral anomaly at the Source, the One reinserts the Path of the One into the programming of the Matrix by choosing 23 individuals to rebuild Zion.

According to the Architect, Zion was completely destroyed 5 times before when Neo reached him. Unfortunately for the machines, Neo broke the cycle and Zion wasn't destroyed the 6th time.

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    Not to mention that in the original plot Zion has been just another layer of the Matrix for people who rejected "the city" one. So from the machine's perspective destruction of Zion is similar to you emptying the recycle bin on your PC.
    – Mr Scapegrace
    Commented May 18, 2017 at 7:15
  • Sorry but you've copied almost verbatim this answer from the Fandom wiki. matrix.fandom.com/wiki/Zion. What is the prime-program and why? What is the "integral anomaly"? What is The Path of the One? A program? What sort of program? a DLL? A hack? Python? Is the Matrix written in C#?
    – Fandango68
    Commented Nov 23, 2021 at 2:59
  • And why 23 people? What's this "23"? Reminds me of that movie with Jim Carrey.
    – Fandango68
    Commented Nov 23, 2021 at 3:01
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The sequels had a very weak plot frankly, if they had the means to brute force Zion entry they should have rather than all the bother of capturing and cracking a human Captain.

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    capturing of morpheus important. only then neo become the one. machines need the one for source.
    – Gomes
    Commented Jun 7, 2017 at 12:33
  • Not weak, just complicated. But @Gomes above me is correct. It seems the only way the machines found to control humans and the 1% of them rejecting The Matrix was to encourage this cycle of hope and "resistance".
    – Nom1fan
    Commented Feb 4 at 10:40

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