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Destroy Ganon is a Main Quest in Breath of the Wild.
It is given by King Rhoam's spirit in the tower of the Temple of Time on completion of The Isolated Plateau quest. Technically, Link can go to Hyrule Castle and confront Ganon at any time from then on, although the King advises against this and directs him toward the Seek Out Impa quest.
While defeating Dark Beast Ganon does cause a completion message to appear on-screen, the defeat of Ganon is not retained in the game world - re-entering the save file will return Link to the moment before entering the Sanctum. However, a star is added to the save file to signify completion, and Kilton's Medals of Honor can only be obtained on a starred save file. Hyrule Compendium photos of Calamity Ganon and Dark Beast Ganon are also retained.