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In The Bourne Legacy, the blue pills enhanced the intelligence of the agents. But did they only enhance intelligence, or did they also affect the agents' behavior?

I remember them saying that the facility was designed for behavioral design.
From the transcript:

And people there are working on behavioral design.
It's programmable behavior, neural design.

Is she talking about the conditioning that Jason Bourne and others went through, or is she also talking about the drugs they gave them?

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She was speaking about some of the various projects that people were working on at the facility. Some of her coworkers were working on programmable behavior, unrelated to the project she herself was working on. While it's possible the blue pills contained that technology, I don't think the film is suggesting that.

The relevant dialogue:

Look, there are projects at Sterisyn, defense projects that could explain why he did what he did. And people there are working on behavioral design. It's programmable behavior, neural design. Do you understand what I'm saying to you? I think he was exposed to something at the lab.

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From that same transcript:

The green side, the physical side, is nothing more than a 1.5 percent rise in your mitochondrial protein uptake. But with 1.5 percent, you see this immediate increase in cellular tempo, muscle efficiency, oxygenation... And the blue side? Intelligence, obviously, but it's more than that. It's neural regeneration and elasticity. Sensory function. Pain suppression.

Thus yes, they did enhance more than just intelligence. But they had no behavioral influence. Like Keen says, that would likely be part of another program at the same facility.

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