Another possibility is a young mage who has a special connection to the darkness. They might start off being curious about the emissary of darkness and end up either helping it or trying to stop it, depending on how their character develops throughout the fanfiction.
It could be the emissary of darkness itself. The story could focus on its journey, its thoughts, and its plans.
Maybe a brave knight or warrior who is determined to defeat the emissary of darkness. The story would then be about their training, their battles, and their inner struggles as they face this powerful foe.
Well, in 'emissary of darkness fanfiction', a cool concept could be the relationships it has with other characters. It might form an unlikely alliance with a hero who is trying to understand its motives. Also, the idea of its lair. Is it a dark, foreboding castle or a hidden dimension full of darkness?
Another possibility is that it could be Zelda herself. She is a powerful character with magic abilities. She could be the main character trying to use her powers to stop the Keeper of Darkness from plunging Hyrule into eternal darkness.
A regular person, say a factory worker in a dystopian society where there is no hope. One day, she discovers a secret resistance group that is trying to change things. She decides to join them, and through her own growth and the group's influence, she transforms from a despairing individual to a beacon of hope for others. This shows how an ordinary person can be the main character in such a story.
One possible main character could be a young, wayward wizard who has been seduced by the power of darkness. He starts as an apprentice in the Mystic Force but is lured to the dark side, becoming the master of darkness. He would then be at the center of the story, with his actions and decisions driving the plot.
Maybe it's an existing side character from the Yugioh series, like Bakura. Bakura already has a connection to the dark side in the original series. In this fanfiction, he could be further engulfed in darkness, becoming the 'aff'. His struggle between his good side and the dark forces that are taking over him could be the central focus of the story. He would have to use his knowledge of Yugioh dueling and his inner strength to break free from the darkness.
Three Realm Emissaries: The Three Goddess Sisters. The main character's father was an envoy of the three realms. In this urban novel, the protagonist, Zhang Hao, lost his father when he was young. Later, he found out that his father was not only alive, but he also met a strange person to treat his illness. This allowed him to obtain the cultivation of his ancestor for 300 years and become the envoy of the three worlds. Although the three beautiful sisters of the Three Realms Emissary had reached the peak of their careers because of Zhang Hao's help, father and son could not recognize each other. I hope you like this fairy's recommendation. Muah ~😗
Blake could also work well as the main character. Given her past and her connection to the White Fang, she has a lot of internal conflict. The God of Darkness could either prey on that conflict or offer her a way to resolve it in a way that is both tempting and dangerous. This would make for an interesting exploration of her character.
I don't know for sure since I haven't read it. But likely, the emissary would be one of the main characters. There might also be the people or entities that the emissary is sent to interact with, like a king or a leader of a certain group.
A powerful sorcerer who wants to control the power of the fairy of darkness for his own evil purposes could be a great antagonist. He might try to trap her and force her to do his bidding.
It could be an ancient evil that has been lurking in the shadows for ages. Maybe a dark spirit that was sealed away long ago and is now breaking free, and Naruto has to control the darkness within himself to fight it.