I like Honoko's idea best so far. Maybe Danzo and Madara previously fought and both came back damaged. Danzo took his eye in the process but injured his arm. Most likely they were working together, but Danzo betrayed him. Everything would make sense with that.

Has anyone played the brothers scenario, yet? Did we ever find out if Madara's brother died? What if Danzo and Tobi are brothers, each sharing an eye?

Btw, this is completely off subject, but why on Earth did Madara help annihilate the Uchihas? Why would he care if they rebelled? Itachi wanted peace when his clan was brooding for war, so he did what he did. But wouldn't Madara want the coup to happen so that the Uchihas could be in charge?