Board Thread:Theories and Speculation/@comment-1783334-20150507053750/@comment-25227224-20150507065400

Shisui had one eye BEFORE it was given to Itachi and it still had the Mangekyo form. He probably used it on Itachi to make him believe Shisui died and went into hiding which explains why it needed to recharge since Shisui never had a chance to use it on anyone

It was destroyed by Itachi when he killed the crow. The other eye was in Danzo's possession. It was also destroyed by Danzo.