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During his life Shisui received praise as the most gifted Genjutsu user of the Uchiha cla of his generation, his ocular powers even excelled that of Itachi Uchiha. This caught the attention of Danzo the leader of . the secretive ROOTS division of ANBU, whom he willing gave his right eye to. His left eye was then given to Itachi before he committed suicide in such a manner that no possible DNA existed outside his two sacrificed eyes in order to prevent being resurrected using the forbidden technique Edo Tensei. His second eye has just made its appearance in Naruto chapter 550.
Mangekyou Sharingan; Shisui possessed the unique ability to rewrite a person's personality from within. Unlike a traditional mind control where the victim was aware of the control being pushed on them, this technique would permanently change the personality making the person willing to accept the changes to decisions or way of thinking. It was so powerful that even another Uchiha with a Mangekyou Sharingan could not detect the attack when applied to him or herself. However only Shisui himself could trigger the technique according to Itachi outside of Hashirama's chakra the technique could only be activated once every decade. In the end Itachi hoped to use it as his trump card to stop Sasuke should he fall under the dark influence of Uchiha Madara.
Outside of his genjutsu Shisui was regarded as a highly skilled Shinobi in hand to hand combat. Upon which having perfected the Body flicker technique to the point that only the Fourth Hokage outmatched him in speed using his Time Space jutsu.