Hmm....makes me wonder if Danzo was capable of using the Mangekyo as well. As this is a Mangekyo technique it suggests he had access to the MS. Also Itachi comments how the technique takes a decade to recharge, unless the person has access to Hashirama's power, a pretty clear reference to Danzo.
This chapter also makes me question the idea that to unlock your MS you need to kill your best friend. Out of Itachi, Sasuke, Shisui and Kakashi, not one of them killed their best friend to achieve the MS.
It also brings up the question of how Yagura, the Mizukage was being controlled. Kisame said the Mizukage was being controlled by the Sharingan and Mei said she thought Danzo's mind control was similar to what was controlling Yagura. This made me think that maybe Madara somehow got a hold of Shisui's other eye and used it, but that can't be the case now since both eyes are accounted for.