What happens is eventually ganon is revived. (other than having links blood sprinkled over his ashes.) He begins to spread darkness over hyrule. Halfway through the game link tries to fight ganon in hyrule castle and discovers that ganon can't be beaten by the master sword anymore. So link has to power up the master swords with the courage of farore, the wisdom of Lanayru, and the power of Din. He then confronts ganon in hyrule castle, which has now been turned in to ganons tower, in the end link beats ganon and returns peace to hyrule. Hope you liked it!