Originally Posted by poopdeville
The real secret of the magnekyou sharingan is that you need to kill your best friend to activate it fully. The more epic the battle is, the more awesomest the sharingan becomes. Madara engineered a situation where Sasuke is going to have to fight to kill Naruto. But it turns out that Sasuke has been on a super secret ANBU mission since the Chuunin exam. This, of course, is why Sasuke was allowed to leave Konoha so easily.
Having completed his primary mission objective of spying on/containing Orochimaru, Sasuke pursued his secondary mission: infiltrating Akatsuki. Itachi and the Hokage hoped to expose the cause of the Kyuubi attack, and realized that the Akatsuki leadership would be interested in anybody capable of killing Itachi, so they staged his death at Sasuke's hands. Now Konoha has three magnekyou sharingan. (Well, 5, I guess) Indeed, the Konoha team didn't find Itachi's body.
Seriously, Itachi = Snape, Sandaime = Dumbledore.