Here's my take on everything:
We all know that Danzo and the Village Elders ordered Itachi to kill the Whole Uchiha Clan because they were planning a major coup and takeover of the Leaf village, but why were they. I think that Danzo had something to do with it. We know that he hates all of the past kages (perhaps not the 4th though, but maybe) and has secretly and openly lusted for the position of kage himself. He may have leaked lies and things to the Uchihas (like things like the Hokage was already planning a major killing of them, or was planning on banning them from the village, etc. Things of that nature.).
We also know that Danzo is looking for Kabuto because he knows of his connection to Orochimaru and whatever dealing that he did with Orochimaru may likely get his Kage status revoked and him jailed/killed/whatever else they may see fit to do to him.

He also said that it has to do with his right arm as well. As to what that may be about, I have no idea. Maybe something similar to how Oro lost his arms to the third Hoakge's Sealing jutsu happened to him.
Now for my Theory.
Theory: I believe that Danzo wanted one of the Sharingans so badly, he used Itachi to kill everyone and obtain on of the Sharingans. He could have then had Oro and Kabuto implant it into his already messed up eye (remember he already was wearing the wrap when he was with Hanzou.) You may ask why Oro never tried to get his body. It could be because his body was already broken. He was missing an eye, he was old, and he may have already have messed his arm up at that point. The only flaw with this theory that I can find would be why didn't Orochimaru get the Sharingan himself since we all know he craved one. I think that he may have only been able to retreive that one eye because the person had to been near death to get it (if you could get a sharingan after someone died, Oro would have been had one. He could just go find a grave of a recently deceased Uchiha and take it). He may have transplanted it into Danzo because he may have some Bad Ass Jutsu that Oro wanted for himself. If he could get the Sharingan, and some secret amzing jutsu in one go, why would he risk harming him self for it? He may HAVE tried to take Danzo's body, but was injured in the attempt and may have injured Danzo's arm in the attempt as well (that could be how Danzo's arm is connected to Orochimaru).
Any thought on this theory?