Guess: The Sharingan & Kyuubi
Ancient Japanese creations myths help explain the relationship that exists between the Sharingan and Kyuubi. Izanagi, one of the creation gods, lost his wife when she gave birth to Kagutsuchi (fire-child/god of fire.. what suspect to be inspiration for Kyuubi) and burned to death. He visited her in hell, and came back and had to wash himself of the evil from Hell, and thus Amaterasu, Susanoo, and Tsukiyomi were born. This story explains why Kishi felt it important to have Uchihas kill/lose a loved one in order to obtain Mangekyou Sharingan to render the techniques of Amaterasu, Susanoo, and Tsukiyomi. So there has been an established relationship between Sharingan and Kyuubi.
Pertaining to the manga, there has been speculation that the Sharingan created or is closely tied with the Kyuubi due to Madara controlling it when he fought Shodai Hokage. And since Shodai controlled all the other Bijuu, most of us cannot help but think there is something special about the Sharingan that enabled Madara to have more control over Kyuubi.
Now in 460, we see a darkness engulf Sasuke, which looks a lot like Kyuubi pre-skeleton.
It seems Tobi (I refuse to say Madara till it is known with doubt) sent Zetsu to rat out Sasuke to make him angry and to really bring out his darkness through anger. Tobi knows Sasuke has absorbed a lot of darkness and negative energy since he was young (i.e. Itachi telling him to cling on to life through hate) and the fight between Raikage and Sasuke will create more anger and hate.
So what? It has been said that Kyuubi appears where human malice collects and festers:
Malice has indeed collected and festered within Sasuke!
My point: Perhaps Tobi is re-creating yang Kyuubi chakra by using Sasuke's malice, and then plans on somehow joining it with the Yin within Naruto?