Board Thread:Theories and Speculation/@comment-1512913-20150221101637/@comment-25549954-20150301203627

It is not stated directly anywhere but it's just my theory, it is based loosely on Tobirama's statement, Tobirama said "When an Uchiha suffer after experiencing the loss of loved ones or despair special chakra sprout inside their brains, which affects the optic nerve and produces the change in their eyes, ...the eyes that reflect the feelings... the Sharingan." Same case for Mangekyou but it requires extremely painful experience. It probably changes chakra pathway or even more. Don't take it seriously it's just a theory.

Now I'll go a little deeper, all I'm saying is that at the time of Mangekyou activation special chakra sprouts and something changes even more, the optic nerve is affected so the person goes blind after overuse, and the third power Susanoo is unlocked this power is notjust only from Right or Left Mangekyou but from both eyes as Sasuke said, we have seen Itachi and Madara not having their Mangekyou activated when they activated Susanoo, so I think it is not something related to eyes but body, as the ability retains even after the eyes are not activated or absent, and it has something to do with the changes in the body, Uchiha chakra increases perhaps, but Kakashi a non Uchiha managed to awaken Mangekyou so basically any chakra is able to awaken Mangekyou for an implanted Sharingan and I believe he got accustomed to those eyes because a lot of his technique depended on Sharingan, and all techniques require chakra pathway to work right? since the chakra flows in certain different pathways to create a technique, and the hand seals manipulate the amount of chakra required. I believe his chakra pathway is set to use Susanoo again so that it retained the ability.

In simple words its not just the eyes that changed but chakra network after the activation. I didn't say Susanoo changes the pathway but his Mangekyou Sharingan did.