In The Legend of Zelda: The Wind Waker, set hundreds of years after The Legend of Zelda: Ocarina of Time and within the Adult Link Timeline, the gods have flooded Hyrule, creating the Great Sea, encompassing the highest mountaintops of Hyrule. At the beginning of the game, Link's younger sister Aryll is captured by the Helmaroc King, a giant masked bird that mistook her for the pirate captain Tetra. After some persuasion, Tetra agrees to help Link chase after the Helmaroc King in order to rescue Aryll, during which Link discovers that the bird is under the control of Ganondorf, who is revealed to be searching for Princess Zelda. However, before he can clash with Ganondorf, Link is launched into the Great Sea by the Helmaroc King. After being saved by the King of Red Lions, Link then undergoes many trials, which includes acquiring the Wind Waker and rescuing Aryll, which results in The King of Red Lions bestowing him the title "Hero of Winds".
With Aryll safely on board Tetra's Ship alongside the pirate crew, Link discovers that his quest is not yet complete, as Ganondorf still poses a threat to the world now that the seal holding his power has been fully broken. Tetra and The King of Red Lions are eventually revealed to be Princess Zelda and King Daphnes Nohansen Hyrule, respectively, the last members of the Royal Family of Hyrule. As a result, Link takes Zelda to the underwater Hyrule Castle to keep her and the Triforce of Wisdom safe, after which he proceeds to restore the Master Sword's power to repel evil and reassemble the Triforce of Courage. Now properly equipped, Link, with additional assistance from Zelda, manages to seal Ganondorf by plunging the Master Sword into his head just before Hyrule is fully submerged within the Great Sea, as per Daphnes' Triforce-granted wish of Link and Zelda having a future. With the world saved and Aryll safely returned to their grandmother on Outset Island, Link decides to accompany Tetra and her crew to set sail for for new lands, with Aryll, their grandmother and the rest of Outset Island's population tearfully saying goodbye while Link reciprocates the heartfelt feeling.
After losing Tetra to the mysterious Ghost Ship, Link embarks on an ocean-wide quest to free her, and later, the Ocean King during the events of Phantom Hourglass.
Super Smash Bros.
Toon Link is an unlockable character in Super Smash Bros. Brawl, in which he can be unlocked by either clearing Adventure Mode: The Subspace Emissary and/or going through the hidden door in The Forest stage, clearing Classic Mode with any character on any difficulty after clearing The Subspace Emissary, or by participating in 400 VS matches.
Toon Link returns as a playable character in Super Smash Bros. 4, now as a starter character. Although fairly minor, Toon Link's design nevertheless underwent changes: his overall design and overall color scheme are sleeker and brighter, respectively, which make him virtually identical to his appearance as of The Legend of Zelda: The Wind Waker HD.
Toon Link returns as an unlockable character in Super Smash Bros. Ultimate. Unlike in previous games, he is now joined by Young Link, with both characters functioning as derivatives of each other in certain aspects.
- Toon Link, Young Link and Cloud Strife are the only swordsmen in the Super Smash Bros. series capable of wall jumping.
- Toon Link is the only playable character from The Legend of Zelda series to have debuted in the 21st century.