I think Shisui's and Itachi's story will be revisited in flashback form. There are too many 'cookies' not too. First, the suicide note. If you look at the drawing, its ripped along the right margin. It could be a sort of puzzle, with the other ripped half revealing the truth. Second, Why would Kishi have Ao mention that Danzo had Shisui's eye and that such a power was controlling the 4th Mizukage? Later, we saw from Kisame's Akatsuki origin flashback, that Madara was standing in the shadows controlling the 4th Mizukage. This was after Shisui was dead because Kisame greeted and welcomed Itachi into Akatsuki. Third, what was the relationship Madara had with Shisui?
My theory is that Shisui was an Akatsuki operative. Madara's pipeline to the Uchiha clan.
He was used to stir up revolt within the clan to sow the seeds of rebellion which would lead Danzo and the Elders to perceive the Uchiha as an immediate threat. All according to Madara's plan for revenge on the Uchiha, mutually removing threats and Harvesting eyes.
He was also used earlier by Madara to put the 4th Mizukage under Madara's control. And while, due to his warping ability, Madara was not found out or discovered by Kirigakure--Shisui was detected on his way out by Ao. The two fought to a stalemate and Ao escaped.
Itachi was the only one to discover Madara's presence in Konoha at the time of the massacre. Had other Uchiha the chance to discover him? Did he walk among them? Or among the Anbu (with his mask and all). Did Itachi also find out Madara had used Shisui as his tool? And was forced to make the VERY difficult decision of Clan vs. Peace? Power vs. Friendship? Chose the impossible path of agreeing with Madara and Danzo that the threat had to be eliminated, with his price for cooperation being his innocent little brothers life? Chose further, to monitor the greater threat in Uchiha Madara from up close, by joining the dark Akatsuki? To be the ultimate counter-weight to an attack on Konoha?
I have no doubt that Danzo and Madara had brokered a deal as to the elimination of the Uchiha and the harvesting of the Eyes. Danzo will make a deal with anyone as witnessed by his collusion with Hanzo of the Rain. His familiarity with Orochimaru and their implied relationship when Sai presented himself as his emissary. Madara and Danzo's greetings when they met and 'fought' also revealed a level of familiarity.
Danzo's price for Itachi's collusion was Shisui's special eye. And and a quantity of Uchiha eyes. Madara's price was possibly Shisui's other eye and the use of Itachi and the remaining eyes. Itachi's price was they both lay off Sasuke and Madara not attack Konoha. The price he paid in exchange was steep. But the alternative was even more unthinkable in his mind.
