Wild Idea.
Tobi isn't madare, but is trying to regain it's abilities.
Tobi is Obito, and recently (during the three year jump), gained the MS sharingan. which caused Kakashi to gain it aswell.
now, just to tie down some strings.

Obito came to to get the secrets of Madare from the Uchiha hideout, but even after killing everybody, he couldn't fing where it was, and was eventually stopped by Itachi, so he goes into hiding once again.
later on, after founding the akatsuki and using conan and Payne to manipulate everyone else, he makes Zetsu follow Sasuke, and then goes by himself to the hideout, and reveals the ultra powers of the sharingan (perhaps by killing the orriginal founder of the akatsuki, or killing and necromansering Payne back to life).