The Legend of Zelda: The Wind Waker ambitiously traded a more traditional Hyrule for the expansive Great Sea - a controversial change, but one that produced a variety of interesting islands to explore. One, in particular, is pertinent to Wind Waker's story yet remains mysterious throughout: Greatfish Isle.
Early in Link's adventure to save his sister from the Forsaken Fortress, his boat and Wind Waker companion, the King of Red Lions, charges him with retrieving the Master Sword. In order to obtain it, Link must first acquire the three Goddess Pearls. The first two require some dungeon delving, while the final is supposedly located on Greatfish Isle, home of the water spirit Jabun, one of Zelda's several talking fish.
When Link and the King of Red Lions arrive at Greatfish Isle, they find the entire island destroyed and no sign of Jabun. Storm clouds constantly swirl above the island, and lighting cracks on the horizon. Little explanation is given about the destruction of Greatfish Isle, aside from the fact that it is the work of Ganondorf, who has cursed the three islands harboring the Goddess Pearls. While this may be satisfactory for Wind Waker's plot, it doesn't offer any answers as to how exactly Greatfish Isle was destroyed.
How Wind Waker's Greatfish Isle Was Destroyed
In the absence of clarification from Nintendo, Zelda theorist NintendoBlackCrisis pieced together a convincing theory on YouTube. They postulate Greatfish Isle was destroyed by the seemingly endless storm summoned by Ganondorf's curse and, more specifically, a great bolt of lightning. The curse tracks because of several lines of dialog; a Rito on the island tells Link "this place suffers under dark clouds and rain," while the rest of the sea "boasts clear skies." The King of Red Lions later mentions "Morning has not broken since [Link] arrived at Greatfish Isle. [...] It is as if time itself is frozen."
As for the curse manifesting lighting to destroy Greatfish Isle, NintendoBlackCrisis looked to other Zelda games for proof of Ganondorf's power. In Ocarina of Time, which Wind Waker heavily references, Ganondorf uses lightning magic in the fight against Link. NintendoBlackCrisis also points to Breath of the Wild's Divine Beast Vah Naboris, which is also afflicted with lighting magic, as proof of Ganon's electrical proclivity.
The manner in which Greatfish Isle was rent to pieces suggests it would require a very powerful attack, and the surrounding lightning storm makes the lightning bolt theory plausible. Unfortunately, it does seem to conflict with Wind Waker's use of the Master Sword, which had sealed away a majority of Ganondorf's power prior to Link pulling it from the pedestal - an event that occurs after the destruction of Greatfish Isle. When considering this, the destruction of Greatfish Isle appears to be a potential Wind Waker plot hole, though not one so egregious as to be a detriment to the narrative. The exact method of destruction used on Greatfish Isle will likely never be known, but all signs point to The Legend of Zelda's Ganondorf magically tearing it asunder.
Source: NintendoBlackCrisis/YouTube