*WARNING! MAJOR SPOILER AHEAD!!*
In Naruto manga chapter 550, all the truth about Uchiha Shisui was revealed, including how he died, and also about his ultimate eye technique that made his eyes a target by Danzou, Orochimaru, and many others who wished to take over his eyes hence gaining the ultimate power that the eyes possessed.
In Naruto Part 1 we learnt that Uchiha Shisui was found dead by a river and was thought to be killed by Itachi for the eyes. However, the truth was revealed in Naruto manga chapter 550 that Uchiha Shisui came to Itachi to give him one of his eyes, after another eye was taken by Danzou (no information on “how” this happened). Uchiha Shisui then made it look like his eyes were already crushed and damaged when he died. Itachi also claimed that Shisui taught him to protect peace as a ‘nameless shinobi’, to protect peace from behind the shadows. So the truth is Itachi never killed Uchiha Shisui, they were both just two brave shinobi’s who dare to protect peace without being called a “warrior”.
When Itachi met Naruto some time ago before his fight with his brother Sasuke, he gave Naruto some of his power. In chapter 550, it was revealed that what he really gave Naruto was actually Uchiha Shisui’s eyes embedded on a crow. However, this eye can only be activated once in a decade. This ultimate genjutsu is powerful enough to break Edo Tensei, and it is called Koto Amatsukami!!
On a side note, since Itachi is already free from Edo Tensei, it’ll be interesting to see him act as his own self and play an important part in the Fourth Ninja War!