Board Thread:Theories and Speculation/@comment-1783334-20150507053750/@comment-26038416-20150507074459

Shisui had no reason to fake his suicide and now to suddenly start coming after Sasuke because he killed Itachi. If Shisui was alive all this time then he would know that Sasuke didn't know anything about the truth and saw the outcome between Sasuke and Itachi. While this hooded man does have a connection to both Akatsuki and the Uchiha (or mainly Itachi anyway) I don't think Shisui is involved.