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In Matrix Reloaded, the Agents target the Key Maker right after Morpheus and Trinity rescue him. Agent Johnson (the one who fights Morpheus on top of the trailer) tries to kill the Key Maker which doesn't make sense since the Agents are programs inside the Matrix and The Key Maker is essential for The One to get to the source. Components of a system work together to achieve a mutual goal.

I understand why the Agents were targeting Neo. Maybe they didn't know about his role in the system and all they saw was that he was "breaking the Matrix rules" and could be a potential problem but as for the Key Maker, surely the Agents know about his role in the system. So why try to stop him?

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    You assume a system as complex as the Matrix has deliberate control over all its many moving parts. You might as well as someone why they are schizophrenic. The answer is "because they can't help it." – Kyle Jones May 20 '14 at 19:00
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    "To get to the other side"? – Valorum May 20 '14 at 19:03
  • "components of a system work together to achieve a mutual goal" -- Does Pandora work with Thunderbird to achieve a mutual goal...? – Brian S May 20 '14 at 19:03
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    Have you never launched a newly-installed program and have Windows Firewall declare that it has prevented it running as a server -- even though both are components of the same system, the latter is deliberately interfering with the function of the former. My speculation is that the Agents are the firewall/anti-virus of the Matrix, and as such they quite likely don't know the Big Picture since they don't need to to do their jobs. – Kromey May 20 '14 at 19:09
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It boils down to two conceivable reasons, both equally likely;

  1. The Agents are largely (or wholly) unaware of 'THE PLAN' and are simply acting on their instructions.

Although Smith (who appears to be the Senior Agent inside the Matrix) seems to have a wider awareness of the history of the Matrix as well as a solid connection with the outside world, part of the conceit of the Matrix trilogy is that "the One" and his acolytes need to be unaware that Zion is simply a system of control until he meets with the Architect.

If the Agents start letting the heroes proceed unchecked, it would immediately give the game away that something was wrong. Junior Agents therefore follow their instructions to cleanse the Matrix of imperfections like exiled programs, regardless of the potential consequences. The system relies on the strength of the One to overpower any obstacles this might present.

It's also quite conceivable that the Oracle would simply come up with a backup plan if the Key Maker dies; "You must now find the Key Maker's Apprentice..." or some other nonsense.

  1. Killing the Key Maker won't actually result in his destruction

It is only Programs whose function is no longer required that are "returned to the source" after their physical shells are damaged beyond repair. As we see from Smith (and the Oracle and several of the Agents) if a program still has a purpose then it is perfectly possible for them to be reconstituted into a new body.

Arguably, the Key Maker's usefulness only ceases once he's led the One to the Architect. It's possible that he wouldn't die if you killed him. He'd simply pop up elsewhere with a new body and a new plan to infiltrate the Architect's lair.

  • So, this is more like an antivirus program trying to shut an application that you trust? If you can't make an exception, you can restart it. – C.Koca Jun 21 '17 at 8:29

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