YuGanon is formed after Yuga resurrects Ganon through the power of the descendants of the Seven Sages, and proceeds to merge with him. As he is about to destroy Link, he is restrained by Princess Hilda, ruler of Hyrule's sister world Lorule. Hilda tells Link to save six of the Seven Sages' descendants whom Yuga turned into paintings. However, it turns out that Hilda covets the Triforce of Hyrule to replace that of Lorule, which was destroyed long ago to prevent wars, in order to save Lorule at the cost of Hyrule.
During the final battle, YuGanon is summoned by Hilda to fight Link take his Triforce of Courage, but he is defeated. As Hilda is ordering him to relinquish Ganon's Triforce of Power to her, YuGanon reveals that he wants the Triforce for himself to remake the universe in his own image. He turns Hilda into a painting and steals the Triforce of Wisdom in order to increase his power drastically. However, Link destroys him, completely obliterating Yuga, and forcing Ganon's soul back into Hyrule.
YuGanon retains Yuga's extreme scorn towards everything but himself, and his obsession about beauty and making people prettier by turning them into paintings, he also keeps Yuga's hair and clothes. YuGanon also displays Ganon's liking for destruction, voice, movements, and fighting style. However, Yuga remains in control and acts the same before and after the merging. YuGanon wields Yuga's powers over paintings, as well as Ganon's Dark Powers magnified by the Triforce of Power.
Like Ganon (and Demise before him), he wants to take over all words and remake them following his design, and is a master of manipulation. However, the fact that he calls Hilda "deluded" upon betraying her reveals that Yuga's loyalty was a pretense for long before the merging. (In the same way as Ganondorf "swearing" loyalty to the King in Ocarina of Time.) Moreover, YuGanon states his intention to "take his place among the gods", while Ganon is more interested in taking their creation for himself.
During the first stage of the final battle, YuGanon fights in the exact same way as Ganon does in A Link to the Past, Oracle of Ages/Seasons, and Four Swords Adventures, by teleporting and attacking with his trident. He will swipe his trident in front of him, infuse it with reddish black dark energy to strike forward or throw it like a boomerang, and disappear to conjure a rain of exploding dark energy balls. Link must dodge his attacks and strike him repeatedly with his sword.After YuGanon gains the Triforce of Wisdom, he starts levitating around and hurling energy balls at Link, which he must strike with his sword to send them back, engaging the classic "Dead Man's Volley". Link must strike the energy ball back and forth until his foe gets hit and turns into a wall-painting. Zelda's spirit then manifests itself and grants link the Light Arrows.
Link must turn into a painting and keep away from the demon, who will charge towards him on sight. Link must fire a Light Arrow at YuGanon to expell him from the wall, before striking him with his sword while he is down. YuGanon will then conjure many energy bats from within the walls before repeating the process.
From then on, YuGanon will fire two energy balls at once, forcing Link to repel them both. When in painting form, YuGanon blocks all arrows fired in front of him and Link must get behind him. The third time, YuGanon keeps away from Link, who must fire his Light Arrow in the opposite direction. (The arrow will go all around the room towards YuGanon's unprotected back.)