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In Episode 336, Itachi was seen to apply his genjutsu on Mecha-Naruto.

But Mecha-Naruto is a robot which does not have a brain but memory chip. As it is a robot (which does not have any chakra), its battle techniques could not be copied by Kakashi's Sharingan.

Mecha-Naruto

Wikia-Genjutsu mentions that genjutsu can only occur by manipulation of chakra of the brain.

Then how does Itachi put genjutsu on a memory chip of a robot?

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Well, when Mecha Naruto went berserk, he was discovered by Akatsuki the next day and brought to Pain, who modified it.

Maybe he put in a chakra network, or something involving chakra, that allowed the Akatsuki to easily control Mecha Naruto. Maybe that's how Itachi placed Mecha Naruto under a genjutsu.

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Mecha-naruto can absorb and contain chakra. This could mean that he has some kind of a chakra system. he also has a eight-trigrams seal in order to seal kurama and this confirms the previous statement. This chakra would in turn be used by his chip for its functioning similar to how the brain uses electric signals flowing through the nervous system.

The chip could be thought of a mechanical brain that uses chakra(it can sense chakra too!)and gives you all reasons why itachi could use genjutsu on mecha naruto.

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The answer for this is that this episode was filler. Chances are since the episode is a filler, Mecha Naruto is affected because fillers are very different from the anime's plot and/or logic itself.

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    Just saying it's non-canonical and doesn't make sense doesn't really answer the question in my opinion. Rather, one should try to make sense of that specific episode, even if its logic lies outside the main series. And in this case, Mecha Naruto appears in the video games, and IG_42 indicated in the comments there could be an answer there. – Shaymin Gratitude Jun 22 '17 at 21:10

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