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When the Gretas, Agent Richard Noble and Agent Victoria Dunwoody, had the intersect uploaded to them, they turned into mindless killers only able to follow protocol, which turned them into a serious liability, as demonstrated in "Chuck Versus the A-Team" when they're unable to make a choice beyond "killing less people" by flying the bomb out of the city when information on the bomb in the episode did not exist in the intersect.

When the intersect was removed from both agents, they immediately smiled and were thankful that it had been removed from them. Considering that the intersect never had the same effect on Chuck, even though they were obviously running the same software (as demonstrated during the Kung Fu scene), why did the intersect turn the Gretas into emotionless killers?

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The reason why the Gretas turned into vicious killing machines is because the program was tampered with. The NCS (lead by Director Jane Bentley) made several "corrections" to the software in an attempt to create a perfect version of it, successfully suppressing everything that could be a liability to an agent. This is hinted at later in that same scene when Chuck tries to walk away with his dad's laptop and gets stopped by Greta (agent Dunwoody). After first refusing to give it up he changes his mind when Director Bentley walks in and says:

I'd do as she says, Mr. Bartowski. Unlike you, my Intersects aren't afraid to pull the trigger.


This is then confirmed and explained in the very next scene.

BENTLEY

(to Chuck)

We've been studying you, as well. Correcting your father's software for your various... limitations.

SARAH

What limitations?

BENTLEY

His emotional sensitivity, his overreliance on his handlers, his inability to terminate targets.

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I guess I missed that line of dialogue! Thanks! –  user1887 Jun 24 '13 at 1:33
    
@kalina You're welcome! –  Tom Jun 24 '13 at 17:27
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