Final Boss

The Final Boss, much like in any video game, is the last obstacle standing in the way of the lead protagonist's mission. Often, the final boss is the mastermind behind the plot of the game, much like the role Ganon recurringly plays in The Legend of Zelda series. Whether their plan is to take over the world, gain the true force of the Triforce, or rid the land of peace and serenity, this final showdown is the antagonist's ultimate chance to destroy the hero. Ganon is the most popular boss of the Zelda franchise, but the games have seen a variety of different lead antagonists. The final boss often has a puppet, or minion who precedes him, like Zant in Twilight Princess or Agahnim in A Link to the Past, who appeared to be the primary antagonist of the game until the plot took an unexpected turn storyline-wise, revealing the main antagonist to be a larger, more influential figure, such as Ganon himself.

Ganon
Ganon is the most frequently recurring final boss of the series, namely because his ties to the Triforce and to Hyrule itself outweigh any other antagonist in any other Zelda title. As the wielder of the Triforce of Power, Ganon assumes an incredible strength, not only physically, but magically as well; his ability to transform the land and its atmosphere to suit his dark desires is a power used in a more positive light by his representative goddess, Din. Throughout the series, Ganon exists in human form as Ganondorf, in pig form (weilding a Trident in some incarnations), and even in beast form in Twilight Princess, using different aspects of the Triforce of Power to morph into stronger, more menacing monsters.

Ganon (or any related incarnation) is the final boss in: (Ganon is also the final boss in the three non-canon CD-i games, Link: The Faces of Evil, Zelda: The Wand of Gamelon, and Zelda's Adventure.)
 * The Legend of Zelda
 * A Link to the Past
 * Ocarina of Time, and Ocarina of Time 3D
 * Oracle of Ages and Oracle of Seasons in a Linked Game only
 * The Wind Waker, and The Wind Waker HD
 * Four Swords Adventures
 * Twilight Princess
 * A Link Between Worlds (Ganon absorbed by Yuga)

Vaati
Vaati is the second-most recurring antagonist in the Zelda series, only after Ganon, appearing in a total of three games. Vaati is a Minish wind mage who uses his dark magic to get his way, in his search for the Light Force of Hyrule through selfish motives. Like Ganon, Vaati also can change form, and has many more physical varieties than Ganon as seen in The Minish Cap, last of which being his intimidating "Wrath" phase. Vaati only appears as an antagonist, however, whenever Link is forced to pull the Four Sword from its pedestal in the Elemental Sanctuary, releasing his spirit, only to be sealed back into the sword during the game's finale.

Vaati is the final boss in:
 * The Minish Cap
 * Four Swords

Non-Recurring Final Bosses

 * Dark Link: final boss in The Adventure of Link as well as a regular (mini-)boss in Ocarina of Time, Four Swords Adventures, Spirit Tracks, and the Game Boy Advance remake of A Link to the Past. In the A Link to the Past remake he appears as a group of four, mirroring the Links of the multiplayer titles; a similar set of Dark Links accompanies Veran at one point in her boss fight. He also sometimes appears as a group in Four Swords Adventures.
 * Nightmare: final boss in Link's Awakening
 * Veran: final boss in Oracle of Ages
 * Onox: final boss in Oracle of Seasons
 * Majora: final boss in Majora's Mask
 * Bellum: final boss in Phantom Hourglass
 * Malladus: final boss in Spirit Tracks
 * Demise: final boss in Skyward Sword
 * Yuga: final boss in A Link Between Worlds
 * Eighth Dragon: final boss in Game & Watch Zelda
 * Uncle Rupee: final boss in Freshly-Picked Tingle's Rosy Rupeeland
 * Majiyo: final boss in Ripened Tingle's Balloon Trip of Love
 * Stallord: final boss in Link's Crossbow Training as well as a regular boss in Twilight Princess.