Shisui is Tobi (Flawless Explanation)
Shisui, under the disguise of Tobi, first convinced Yahiko to form the Akatsuki, this was the beginning of his plan for world peace.
Shisui and Madara are both firm believers in the theory of "restoring the power of the Uchiha Clan." This was what caught Madara's attention so Madara trained Shisui (at a very young age) to carry on his "will of the Uchiha Clan." Apart from The Sage of Six Paths in having the rinnegan, only Uchiha Madara progressed his EMS to a Rinnegan during near-death. This was because the final step to progress the EMS to a rinnegan was to sacrifice one's self. Madara then told Shisui to destroy Madara in order to awaken the Rinnegan, Shisui then killing his mentor awakened his Mangekyo Sharingan. Right before Madara died, he entrusted Shisui with 2 possessions: the Zetsu and the Rinnegan. The 1st Hokage's cell were used to make the White Zetsu (Senju Yang Energy: Vitality) and he used his own cells to make the Black Zetsu (Uchiha Yin Energy: Genjutsu). Madara then asked Shisui to use the Rinnegan to read the stone tablet left behind by the Sage of Six Paths. Shisui took out his Sharingan in his right eye and stored it, then implanted the right Rinnegan into his face. Shisui learned the truth about the ten-tails and the eye-moon genjutsu plan. Madara also asked Shisui to afterwards implant the eye to an infant called Negato Uzamaki who has the senju's blood (this happened some time before the 2nd Shinobi War). Madara, thinking about the future, was hoping that Nagato could revive him this way through the awakening the power of the Rinnegan. Later, Danzo took shisui's right eye & arm, but they never said how. Danzo is not strong enough to take shisui's eye by force (if he was why did he only take one of Shisui's eye?). It was Shisui that made a deal with Danzo to give him his right sharingan and arm in exchange for Obito's (which Danzo has obtained when he read the report of Kakashi's mission) right eye plus to tell Hanzo to betray Yahiko (Jiraiya's disciple). Thus allowing enough power for Negato Uzumaki (whom is a related to the Senju Clan) to summon the Demonic Statue of the Outer Path (during the 3rd Shinobi War). Now the Demonic Statue (which can only be summoned by someone with the Senju's blood + Rinnegan) is under Akatsuki's control; this was the only way to collect the tailed beasts, through that statue. After acquiring Obito's eyes he gained the space-time technique which allowed him to warp through dimensions and he used to Zetsu's power to give restore his right arm. Tobi saw the opportunity to capture the nine-tails during Naruto's birth. Shisui, as Tobi, attempted to capture the nine-tails through his genjutsu but Minato severely injured him with the rasengan and placed a seal to free the nine-tails from Shisui's genjutsu. Shisui then fled and swore that he will obtain the nine-tails through other means in the future. Konoha at this point believed the Uchiha Clan was responsible for the Nine-Tails attack so they forced the Uchiha Clan to live in the corner of the village. This fueled Shisui's rage seeing that the Uchiha clan is being pushed further and further away. He swore to himself that Uchiha Clan will control the world. In order devote copletely to this plan he now have to completely give up his identity as Shisui and completely focus on his second identity as Tobi. So he met up with Itachi whom called Shisui his "older brother." Shisui then used Kotoamatsukami ,before giving Itachi his left eye, to put Itachi in a powerful genjutsu making it appear that Itachi has killed Shisui, so that his cover as Madara would be flawless. Itachi then awakened his MS through this mean. Itachi made a deal with him telling him to spare the villiage and in exchange he will wipe out the Uchiha Clan. Shisui, acting as Madara, complied to hide his identity and also to obtain spare Sharingans (which would benefit his plans by the power of Izanagi). From then on Shisui carried out his plan through the Akatsuki organization that he has created.
Side notes:
*Tobi knows almost everything about Itachi.
*Ao battled with Shisui recognizing his chakra color; Tobi told Kisame he controlled the 4th Mizukage.
*Tobi's left eye is strictly for the use of Izanagi, (protected him from when Itachi implanted Amaterasu to react with Tobi's Sharingan and Konan's explosive tags).
*Tobi joins Akatsuki after Sasori's death with a very goofy attitude. When Itachi died he became extremely serious.
*Tobi wanted Shisui's eye from Danzo and was mad when he blew himself up.
*Kabuto can't find Shisui's body.
