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Gannon, the Prince of Darkness, invades Hyrule with his evil army, seizes the Triforce of Power and attempts to gather the scattered pieces of the Triforce of Wisdom. He imprisons Princess Zelda and keeps her in his lair at Death Mountain. He is destroyed by Link after getting hit by a Silver Arrow, and burns to ashes.
After fighting the Thunderbird in the depths of the Great Palace, Link continues on to claim the Triforce of Courage, but runs into Dark Link. After their battle, Link claims the Triforce of Courage, awakens Zelda, and the game ends.
Ganondorf's hideous alter-ego, Ganon, appears as the villain in The Legend of Zelda: A Link to the Past. Prior to the events of the game, Ganondorf had turned the Golden Land into a horrible wasteland known as the Dark World, using the Triforce. Upon entering his new universe, he was transformed into a beast that reflected his evil heart.
Atop of Ganon's Tower, Link first battles Agahnim, whom Ganon had used to break the seal on the Dark World. Using the Master Sword, Link reflects Agahnim's own magic back at him and ultimately defeats him. Afterward, Ganon flees to the Pyramid. Link follows him and confronts him for the true final battle. Ganon wields a mighty trident, can teleport, and controls Fire Keese when confronted. Using the Golden Sword and Silver Arrows that Link had received from the Great Fairy in the pyramid, Link defeats Ganon and uses the Triforce to restore the Golden Land to its former glory and bring peace to Hyrule.
The exact nature or origin of these evil beings is extremely vague, but their goals are clear. They put the Wind Fish to sleep in order to keep it locked in a tormenting nightmare, and for the island of Koholint to retain its existence so that they may rule it themselves. It is also unknown if they are indeed all separate entities, or if they are just one single entity, DethI, that refers to itself as "we". Whether six or a single entity, the Nightmare has the power to take the shape of a foe encountered in Link's past, including his most fearsome foe, Ganon, and only one physical presence. Its DethI form is the only original shape the Nightmare takes, suggesting that perhaps it is its true form.
Link reaches the central tower of Ganon's Castle and confronts the King of Darkness. Ganondorf shoots energy blasts at Link, but by using his sword, Link reflects them back at Ganondorf, starting a game of Dead Man's Volley. Ganondorf will reflect his energy back at Link until he misses, rendering him stunned and vulnerable to the Light Arrows. Upon being hit, Link can move in and strike Ganondorf with his sword. After enough hits, Ganondorf falls and uses his remaining energy to destroy his castle. Link escapes with Princess Zelda in the nick of time, but as soon as Link approaches the rubble of the castle, Ganondorf appears again, breathing heavily. Using the Triforce of Power, he takes the form of a giant boar-like creature called Ganon and wields two enormous swords. Before Link can react, Ganon knocks the Master Sword out of Link's hand and out of reach, leaving Link to use other weapons against Ganon's tail, his weak point. Approximately halfway through the battle, the ring of fire surrounding Link and Ganon disappears, allowing Link to reclaim the Master Sword. Link uses the Master Sword to land the final blow on Ganon after a few more hits to his tail have been dealt.
After getting on the moon and agreeing to "play" with the child wearing Majora's Mask, Link is transported to a room in which the final confrontation with the essence of Majora occurs. The first of Majora's three forms is simply a giant version of the mask itself. In a brief cutscene, the floating Majora's Mask grows tentacles and attacks Link. Link must hit Majora's backside with arrows or Zora Link's boomerang fins, or if it was acquired, use the Fierce Deity's Mask and shoot beams from the Double Helix Sword.
Majora's Incarnation has arms, legs, a torso, and a small head with a single eyeball; it is more of a human shape than its last form. It performs various dance-like movements and is very nimble, making it difficult to hit. Making the battle even harder is the fact that Majora's Incarnation leaves a trail of afterimages in its wake, making it harder to see where it is. Majora's Incarnation normally attacks by ramming into Link, but it occasionally stops to hurl a barrage of multicolored energy balls from its hands. Three effective strategies are to spin into it as Deku Link, roll into it as Goron Link, or use the Double Helix Sword.
After Majora's Incarnation is defeated, its limbs grow muscular, develop long tentacles, and grows a full head, providing an overall demonic appearance, becoming Majora's Wrath. Its main attacks involve whipping Link with its long tentacles, usually knocking him down, and spinning around, twirling these tentacles around itself. It can also unleash a massive combination attack on him, and extract top-like blades by pulling out the eye in its forehead and leaping across the room with surprising grace. It must be hit with an arrow, the Zora fins, or the Double Helix Sword.
After delivering the final blow, Majora disintegrates, along with the rest of the moon's chambers, and the moon disappears. Majora leaves the mask behind, cleansed of the evil, and back in the possession of the Happy Mask Salesman on the Dawn of a New Day.
Veran, the Sorceress of Shadows, is the primary antagonist of The Legend of Zelda: Oracle of Ages. She, like General Onox, is unknowingly being used by Twinrova to fill the land of Labrynna with sorrow.
The battle with Veran begins at the top of the Black Tower, while she possesses Ambi. The final battle with Veran starts out like the earlier battle with her when she was possessing Nayru. She warps around the room, attacking with fireballs and summoning monsters. Link must use Mystery Seeds to separate her from Ambi's body. He must then use the Long Hook to pull her away from Ambi and use his sword to attack her. Once a sufficient amount of damage has been dealt, Veran will disappear and Ambi will escape.
Before Link can escape, Veran will appear again and attempt to possess him. She says that her humanoid form is her "true form," but she is going to transform into her "true might". She transforms into a giant fairy, destroying all of the pillars in the room and summoning four Dark Links. She flies around the room, shooting fireballs at Link. After this form is defeated, she appears to have died.
As Link, Nayru, and Ralph escape the tower, Veran captures Link using a Wallmaster and attacks him one last time. She transforms into a turtle, a spider, and a bee, but Link finally defeats her. Labrynna is saved, but nevertheless, Veran completes her mission, and the Flame of Sorrow is lit.
General Onox, the General of Darkness, is a character from The Legend of Zelda: Oracle of Seasons. Doing the bidding of Twinrova, Onox threw the seasons of Holodrum into chaos in order to cause enough damage to the peaceful land to light the Flame of Destruction, a necessary step to revive Twinrova's master Ganon.
Link begins his battle with Onox at his castle upon the Northern Peak. Onox attacks Link with a massive morning star and whirlwinds. Once Link deals enough damage, Onox begins using Din as a shield. Link must knock Din away with the Rod of Seasons before he can damage Onox.
Once Onox is defeated, he disappears and the ground crumbles. Link falls into a room below him, where Onox reveals his true form. Link must jump off of Onox's hands and attack a crystal on his face in order to defeat him. After he defeats Onox, Din is freed from her prison. Nevertheless, the Flame of Destruction is lit, and Onox succeeds.
Twinrova attempts to revive the deceased Ganon in the linked ending by lighting the Flame of Destruction and the Flame of Sorrow by causing havoc in Holodrum and Labrynna. By sacrificing Zelda, the ritual would be complete with the lighting of the Flame of Despair and Ganon would be revived. However, after Link arrives, they are forced to sacrifice themselves instead of Princess Zelda, resurrecting Ganon, but since their hearts were not pure, he was instead resurrected as a mindless monster. He fights wildly, unable to control his body. He can only be attacked normally if Link has acquired the Master Sword. With any lesser sword, Link must use a Spin Attack to pierce Ganon's thick hide.
Appearing from nowhere, Vaati, now a Wind Mage (unlike in The Minish Cap) and only taking the form of a large flying eye-shaped monster, takes to kidnapping any maidens he fancies. A number of heroes fight against him, but they all fail to defeat him. One day, Link, carrying a "cursed" blade uses the powers of the sword to split into four beings, and uses this advantage to weaken Vaati and seal him inside the Four Sword.
When Link enters the final room of Ganon's Tower, he finds Ganondorf standing over Zelda. After a brief conversation he transforms into Puppet Ganon. After Link defeats the three forms of Puppet Ganon, Ganondorf retreats to the roof of the tower. Ganondorf confesses his lust for the winds of Hyrule that contrasted the harsh winds of the Gerudo Desert before attacking Link and reuniting the Triforce. Ganondorf attempts to make his wish but the King of Hyrule touches the Triforce first and wishes for the ultimate destruction of Hyrule. Ganondorf laughs madly and attempts to kill Link and Zelda, starting the final battle.
The battle is a sword duel. Ganondorf swipes and jumps around, avoiding Princess Zelda's Light Arrows. If Zelda hits him, he is left vulnerable to the Master Sword. Alternatively, Link can simply parry several times. After a while, Ganondorf will knock out Zelda. This leaves Link fighting Ganondorf on his own. After Zelda awakens, Ganondorf becomes invulnerable to Link's parries and Zelda's arrows. Zelda asks Link to deflect a Light Arrow off of his Mirror Shield. This leaves Ganondorf open to a final blow from Link, who impales him through the top of the head. Ganondorf is struck through the head by the Master Sword, leaving one final statement before he fades.
His body, with the powers of the Master Sword flowing through him, is petrified and left at the bottom of the sea along with the King to wash away with Hyrule.
At the game's beginning it appears the final boss is Vaati, but as the Links progress throughout the game, it becomes apparent that there is another force threatening Hyrule. When Link arrives at the Desert of Doubt he learns of the Gerudo named Ganondorf who stole the Trident from the Pyramid. The Links continue their journey and face Vaati in the Palace of Winds. After Link defeats Vaati, the Tower of Winds starts to crumble, and Link and Zelda travel down the tower back to Hyrule. However they are stopped by Ganon, who faces Link in battle. As the battle progresses Ganon becomes immune to the Links' attacks. Using an arrow and Zelda's magic the Links defeat Ganon. After he is defeated, he is locked within the Four Sword.
Vaati once again plays the role of main antagonist and final boss in this game. After absorbing the Light Force from Princess Zelda, he attacks Link in his first form, Vaati Reborn. Using his sword Link destroys the orbs surrounding Vaati and strikes his vulnerable eye. Vaati then proceeds to transport Link to a different location and battle him again in his second form, Vaati Transfigured. Using his Bow, Link reveals Vaati's weak spots and attacks them all at once after splitting into four clones using the power of the Four Sword. Vaati disappears, seemingly defeated, and Link frees Zelda. As they attempt to leave the castle it begins to fall apart. Finding the entrance sealed Link and Zelda race to the Elemental Sanctuary only to be confronted by Vaati once again in his third form, Vaati's Wrath. Using the Cane of Pacci and a Picori Portal, Link destroys Vaati's arms and once again uses the power of the Four Sword to reflect Vaati's attacks back at him, defeating the tyrant once and for all.
Link and Midna arrive at the top of Hyrule Castle. Waiting for them is Ganondorf. Using twilight magic, he possesses Zelda, and a battle similar to battles with Phantom Ganon ensues. At Possessed Zelda's defeat, Midna uses the power of the Fused Shadow to purge her body of Ganondorf. Ganondorf changes into his beast form, Ganon. Ganon charges after Link through Twilight Portals, appearing from random portals after a small delay. Link fires arrows into Ganon's head, leaving his stomach susceptible to attack. Link morphs into his wolf form and, with the help of Midna, throws him to the side, and attacks his stomach. After Ganon is finished, Ganondorf jumps on his black horse, and runs around Hyrule Field, spawning ghost minions to attack Link. Zelda aids with the Light Arrows given to her by the four Light Spirits, also riding on the back of Epona.
In the last battle, Ganondorf erects a barrier around himself and Link to prevent Zelda from intervening. As soon as he gets into a fighting stance, sandstorms blow and lightning flashes. His attacks include simple stabs, what appears to be Link's spin attack, and a charge that Link may jump into to initiate a sword lock. To defeat him, Link must either win a sword lock or attack him from behind until he is on the ground (which can be done with the Fishing Rod), at which point Link must execute an Ending Blow.
Link confronts Bellum at the bottom of the Temple of the Ocean King. He battles Bellum on several floors and using Ciela's powers, stops time and defeats Bellum. Thinking Bellum is dead, Link and Ciela return to the surface to restore Tetra to her original self, but Bellum follows them and kidnaps Tetra. Bellum fuses himself with the Ghost Ship and Linebeck follows him in his own boat. Using the cannon, Link and Linebeck destroy the Ghost Ship and enter its remains to find Tetra. Still living, Bellum surprises Link and Linebeck, attacking them and destroying Linebeck's boat. When Linebeck attacks Bellum's tentacles with the Phantom Sword while Link and Tetra are imprisoned by Bellum's tentacles, the creature gathers darkness around him and makes him take the form of a giant Phantom. Bellum then attaches to the Phantom Linebeck's back and begins the battle. Using Ciela's powers again, Link defeats Bellumbeck and ultimately destroys Bellum.
When Link and Zelda travel through the Dark Realm in the Spirit Train, they are attacked by the Demon Train. Using the cannon attached to the Spirit Train, Link blows off sections of the Demon Train one by one as it tries to drop Bombs onto the tracks. Link then has an option to hit the train's face. After enough hits the back carriage falls off and Link must blast away the second carriage, which shoots laser beams. With enough hits the Demon Train eventually stops. Link and Zelda in her Phantom form climb on to the Demon Train to confront Malladus and Chancellor Cole. The Demon Train starts moving again while Zelda and Link try to get loose enough to use the Bow of Light on Malladus. Using Zelda as a shield against Malladus' attacks Link stops Cole from possessing Zelda. Eventually they reach Malladus and Zelda grabs him allowing Link to use the Bow of Light. The Demon train sinks into the Dark World and everyone appears outside. Malladus loses Zelda's body allowing her to reclaim it. After a failed attempt to take Zelda's body back, Malladus eats Chancellor Cole and transforms into a giant beast. Zelda decides to use the power of her Hylian blood to weaken Malladus and asks Link to protect her by deflecting the fireballs Malladus shoots. After Zelda gathers enough power she and Link use the power of the Spirit Flute and other Lokomos' instruments to weaken Malladus and give him a weak spot on his back. Link then distracts Malladus while Zelda shoots him in the back with the Bow of Light to injure him. After three shots he becomes stunned allowing Link to strike off one horn. They repeat the process twice and defeat Malladus by together pushing the Lokomo Sword into his head.
Demise is originally sealed in the form of The Imprisoned, until his servant Ghirahim revives him in the past. Demise forces Ghirahim into his true form as his sword, impressed that Link has the courage to face him. He challenges Link to a battle. In the boss room, Link and Demise fight using Skyward Strikes. After being weakened by Link, Demise is defeated. Before being sealed into the Master Sword, he vows that he will be "reborn" and he will "destroy" Link.
When Demise dissolves, he is locked inside the Master Sword, and the weapon is sealed away so Demise may fully dissolve.
After traversing Lorule Castle, Link finds Princess Hilda, who takes the Triforce of Wisdom from Princess Zelda's Portrait. She then tells Link that she requires the Triforce to restore her kingdom. She demands Link give her his piece, and commands Yuga, who has merged with Ganon (thus having the Triforce of Power), to attack Link. After Link defeats him once, he reveals that he was planning on taking the Triforce for himself the entire time, turns Hilda into a portrait, and takes the Triforce of Wisdom from her. He then battles Link again, now even more powerful due to having two Triforce pieces. During the battle, Zelda gives Link the Bow of Light, which in conjunction with the Master Sword, he uses to strike down Yuga once and for all.
In Hyrule Warriors Legends, Phantom Ganon is the final boss in Legends Mode as he is fought at the end of the Wind Waker storyline. In addition to no longer being the final boss, Ganon is no longer playable due to the absence of Challenge Mode in Hyrule Warriors Legends.