Cyclone

A Cyclone is an object appearing in The Wind Waker and Phantom Hourglass. Although they are harmless in The Wind Waker, touching a cyclone in Phantom Hourglass causes damage to Link's ship. They can only be found while out in the sea.

The Wind Waker
In The Wind Waker, the deity Cyclos harnesses the power of cyclones. After his monument in Dragon Roost Island was destroyed, he dedicated his life to using his control over cyclones to wreak havoc on all who encountered him. Link can find Cyclos in a humongous cyclone throughout various islands of the Great Sea. If he sails close to it, Cyclos will draw him in, giving Link a slim chance to defeat him with his bow before being blown away into another part of the Great Sea. If Link succeeds in defeating Cyclos, he will be impressed with his skills and teach the young hero the Ballad of Gales, allowing Link to use the deity's cyclones to warp to different islands in the Great Sea..

Smaller cyclones can also be found throughout the sea. They are harmless and, if Link's ship runs into one of them, it will cause the King of Red Lions to change his direction. Some of these cyclones will allow Link to gain altitude if he approaches them while floating with the Deku Leaf, mostly in the Bird-Man Contest.

Interestingly, whenever Link warps using the Ballad of Gales, Cyclos appears under his boat while he is floating up. This is not normally visible and a camera hack must be applied in order to see this.

Phantom Hourglass
In Phantom Hourglass, the smaller cyclones are hard to see at times, which is their only real strength. They have no attacks and can only hurt Link's ship if he sails into them. They can be destroyed if Link shoots them with his cannon two times.

The bigger cyclones are rarer to find and mostly serve as obstacles to impede Link from accessing certain islands. To make the cyclones disappear, Link has to complete certain dungeons or obtain specific items, such as obtaining the Regal Necklace to eradicate the cyclone preventing entrance to the Isle of Ruins. If Link obtains the Cyclone Slate and has the necessary symbols from the Golden Frogs, the young hero can ride a cyclone to warp to a different sector of the World of the Ocean King by drawing the correspondent symbol.