In the manga where Sasuke fights Danzo, we see that Danzo keeps preserving his chakra. It can be presumed that he just did not want to waste even a teeny bit on Karin, but Madara who has been observing quietly comments that he must be preserving it for "something".
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That "something" is revealed to be the intention to deal with Madara.
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Now, isn't it strange that he keeps thinking about Shisui's eyes, telling himself that it is the only way he can fight Madara, and then dies without giving anyone as much as a glimpse of its powers. It is unlikely that a shinobi relies on a super haxxed jutsu and dies not even making an attempt to use it as a last resort.
Later we see Madara over Danzo's body saying that he destroyed Shisui's eye while trying to Suicide bomb him and Sasuke. A possible theory is that Danzou used his trump card, some kind of uber-genjutsu like Koto Amatsumi to fool two top class uchiha's of his death.
In this panel, when all is lost, Danzo opens his right eye.
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I suspect around this time he cast his Genjutsu on the two ninja and one kunoichi present. There is some kind of confusion in the page above, and the one next to it. As soon as Danzo uses Shisui's eye, Madara comments that he used it to make a shunshin-like move, thus wasting it, like all the Izanagis he wasted.
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But I think at this moment. The genjutsu had already been cast. Remembers that Shisui's Genjutsu is so powerful that its victims aren't even aware that they are being victimized.
Two issues remain to be addressed.
1. Madara standing over Danzo's corpse and saying he destroyed Shisui's eye.
Medical experts of the Hidden Cloud, including their Kage and best sensor (as he is "C", I presume he is tops after "A" and "B(ee)"), were fooled by Kisame's "death" which turned out to be just an ordinary decapitated Zetsu. Since Danzo had Shodai's cells, and had experimented and transplanted his body to such an extent that he could perform rare and forbidden sharingan techniques, I presume, he should be capable of pulling off the Zetsu trick as well.
2. Root members find out that their curse mark has disappeared.
Shisui's genjutsu is powerful enough to fool a high ranking forbidden curse/jutsu as the Edo Tensei. I assume it might be pwoerful enough to erase any evidence of his life (i.e without him actually dying) and even "fool" the tongue curse marks into disappearing.
