Quote:
Originally Posted by Shiryuu
Shisui's genjutsu doesn't override his free will. If it did, he wouldn't be going after Kabuto and would just follow Naruto wherever he goes since he's the main goal of the war.
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Itachi wants to protect Konoha so in a way he's doing what he wants but he may not have full control of himself.
Shisui's genjutsu was going to make Sasuke protect Konoha if it was used on him which is a example of how the genjutsu can control people and take away their free will by making them do something.