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In the Mass Effect franchise, at the end of Mass Effect 3, you have the possibility to select the Synthesise option, therefore stopping the cycle and avoiding war between organics and synthetics. The AI had this ability all along but decided to continue the cycle of harvesting nonetheless.

Why did it not choose by itself to apply this to all beings in the galaxy and therefore making the harvest unnecessary?

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According to the Catalyst, the reason that synthesis was not done sooner is:

Because the organics were not ready. It is not something that can be... forced. You are ready. And you may choose it.

Apparently the Catalyst had attempted synthesis previously and failed. Shepherd's "energy" is needed, for this solution to work. See also this answer to a related question.

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