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Madara told Sasuke that the Kyuubi incident was of natural cause and the village wrongly believed that the Uchiha were involved. Both Itachi and Minato confirmed that it was Madara who was controlling the Kyuubi that night, resulting in the Hokage's death, Naruto's transformation into a Jinchuuriki and the village suspicion of the Uchiha.

Itachi also said that Madara took his brother's eye by force, it is still unconfirmed if that is true.