Itachi was ANBU.
I believe he was in root, why?
Because Danzou uses hidden blood mist methods whereby to become root fully you must kill your "brother" or the student you worked with in training.
I believe Itachi and Shisui were both working as root-to-be's and Itachi won.
Itachi then realised he had without knowing, achieved the mangekyou sharingan.
Danzo after the fight saw pieces of shisui that still might work, and got orochimaru to graft the leftover pieces onto his disabled body
I believe he was in root, why?
Because Danzou uses hidden blood mist methods whereby to become root fully you must kill your "brother" or the student you worked with in training.
I believe Itachi and Shisui were both working as root-to-be's and Itachi won.
Itachi then realised he had without knowing, achieved the mangekyou sharingan.
Danzo after the fight saw pieces of shisui that still might work, and got orochimaru to graft the leftover pieces onto his disabled body