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Legend of Zelda and Adventure of Link
Link first learns about Ganon and his plot to take over Hyrule after saving Impa and learning of the quest that he must go on in order to save the land. He travels around Hyrule and collects the eight fragments of the Triforce of Wisdom. Link is able to open the seal to Ganon's lair and uses his newly acquired silver arrow to defeat him. Ganon's minions attempt to revive him which requires killing Link but they are unsuccessful.
A Link to the Past
Link encounters Ganon multiple times through the wizard Agahnim who is possessed by Ganon. The hero first learns about Ganon as he is traveling through the Dark World and saving the maidens. After defeating Agahnim for the second time, Ganon reveals himself and flies to the Pyramid of Power. Link follows him and manages to defeat the king of evil.
Ocarina of Time
Link has a nightmare about Ganondorf before the two even meet. This nightmare later comes true when Ganondorf is chasing after Princess Zelda. He stops to ask Link for directions and knocks him down when he stands against him. Link then goes to open the Door of Time and pulls the Master Sword which causes him to be sealed in the Sacred Realm for seven years. Ganondorf follows Link and snatches the Triforce of Power. Link wakes up seven years later, and after awakening the sages, manages to defeat Ganondorf who is then sealed by the sages. However, in another timeline, Link is killed by Ganondorf.
Oracle of Seasons and Oracle of Ages
Ganon is dead at this time but the evil witch twins Koume and Kotake have a plan to sacrifice Princess Zelda in order to revive. Link learns of this and manages to save Zelda and stop the ritual at the last second. The evil sorceresses then become desperate and sacrifice themselves instead. Ganon is revived but is insane and Link manages to kill him once again.
After spending some time being sealed away by the gods, Ganondorf manages to break out of the seal and threatens the Great Sea. The king of evil has his bird minion capture multiple girls with long ears, including Link's sister Aryll. Link obtains the Master Sword but is unable to defeat him because it lost its power. Link later restores power to the sword and obtains the Triforce of Courage. Ganondorf remarks that Link must the reincarnation of the Hero of Time and the two battle. Link manages to kill Ganondorf in the end.
Four Swords Adventures
At this point in the timeline, Ganon has already been killed but is eventually reborn. Link pulls the Four Sword and is mostly after Vaati but learns about Ganon when he finds Deku Scrubs chanting his name in the Lost Woods. He searches in the desert and finds that he stole the Trident of Power. It turns out that Ganon is actually behind Vaati's return and Link is forced to defeat him once again.
On this timeline, Ganondorf was exposed by Link before he can even attempt to take over Hyrule as the latter had been in the future and warned Princess Zelda. The evil king was slated to be executed but ended up being sealed in the Realm of Twilight instead. Generations later, a new Link is born and Ganondorf later breaks free through the help of the Twili Zant. Link eventually obtains the Master Sword and battles Ganondorf multiple times, killing him in the end.
Despite the fact that the two are enemies, GanonLink is a rather popular Zelda pairing and is probably one of the more popular slash pairings in the fandom. It is an obvious enemyship as it involves the main protagonist with the main antagonist. Link has killed Ganondorf numerous times and Ganondorf manages to kill Link once on one timeline. However, this does not stop fans from shipping them together as they believe that Ganondorf can see the light and that the two can overcome their destinies.