Kakashi had noticed that brief flicker of unease on Sasuke's face. He sighed inwardly. So it really is as I thought.
It was fair to say that aside from Shinji, no one in the Shinobi World knew that the Sharingan in Kakashi's eye was actually a Mangekyō Sharingan that possessed a rare Space-Time Dojutsu.
No one would ever have guessed that a transplanted Sharingan could awaken into a Mangekyō in someone without Uchiha blood, like Kakashi!
After realizing that the Sharingan in his left eye was a Mangekyō Sharingan, Kakashi had quietly experimented with it while also requesting access to the village's top-secret Sharingan records.
As Sasuke's Jonin instructor, Kakashi's request was naturally approved without delay.
That was how he came across a wealth of top-secret records on the Sharingan, and even the Mangekyō Sharingan, dating back to the Second's era.
With the help and confirmation of those records, he had quickly learned how to use his Mangekyō Dojutsu and had also uncovered many of the Mangekyō Sharingan's traits.
The most crucial discovery was that the Mangekyō Sharingan gradually lost its light with use!
The revelation had horrified Kakashi. At the same time, it had given him a way to determine whether Sasuke was the Akatsuki Organization's "E": test his eyesight.
If Sasuke wasn't the Akatsuki Organization's "E," then, having remained in the village all this time, he shouldn't have used his Mangekyō Sharingan more than a few times. His eyesight, therefore, shouldn't have deteriorated.
But if Sasuke really was the Akatsuki Organization's "E," as the Fourth Raikage had accused, then he must have used his Mangekyō Sharingan many times. That would mean his eyesight had likely begun to suffer, at least to some degree.
Kakashi was deeply conflicted by the answer he'd found.
Sasuke and Shinji were the last