Thread:Great Achlus/@comment-26367861-20161006004355/@comment-26367861-20161006033129

itachi never wanted to kill all the uchiha... he was forced into a certain position... as for danzo the uchiha spared would go into hiding or documents would be forged by itachi presuming the survivors dead and/or missing. There are numerous ways danzo wouldn't find out. Besides there are others on this site with Uchiha characters whom survive the massacre. This is fanon, not canon.

as for an explanation in the itachi shinden novel and anime adaption there are a few quotes that hint others survived.

"protect the village and the uchiha name." -Shisui Uchiha to itachi

"the body count doesn't match up, its as if they disappeared." -Itachi's clones to danzo

"i'm a double agent, i saw through both the eyes of the uchiha and the hidden leaf, in the end i didn't know who's spy i was." -Itachi to his anbu subordinates