This is but one ancient legend...
Once, about 7000 years ago, a minish wind mage named [colorpurpleVaati terrorized Hyrule, capturing one maiden after another. A boy named Link sealed Vaati in the mythical Four Sword, created by the picori, a.k.a. the minish.
About a century later Vaati was freed by a tricked new Link. Link, along with his three clones defeated Vaati, but Vaati died under unknown circumstances.
Was that the end of evil? No. A new evil named Ganon, who was far more powerful than Vaati, was sealed in the Four Sword, with the Four Sword sealed forever. Ganon raided Hyrule time and time again, now the master of darkness. The gerudo king Ganondorf became the ultimate master of darkness Ganon. Dying again and again.
By the time of Ganon's last death, now a true master of dark sorcery, imprisoned his power in the Dark crystal Ganon's most powerful creation. His remains in a dark bottle.