At some point in the past, Shisui fought with Ao. Ao retains an acute memory of Shisui's chakra and ability to control others with his Sharingan. Because of this, he recognizes that Shisui's right arm and eye were transplanted into Danz?.
About six months after joining the ANBU, Itachi began to act oddly, and Shisui was instructed by the Konoha Military Police Force to keep tabs on him. Soon afterwards Shisui was found drowned in Nakano river with a suicide note stating that he was tired of carrying out the clan's duties. The police suspected that Itachi had murdered him and used his Sharingan to fake the suicide note, since Shisui was very devoted to the clan, and suicide would have been highly unusual and uncharacteristic. After this, Danz? took Shisui's right arm and Sharingan and implanted them into himself. Itachi later confessed to Sasuke that he did kill Shisui and forged the suicide note, all in order to awaken his own Mangeky? Sharingan. Shisui's corpse has apparently disappeared, as Kabuto Yakushi cannot locate it.