The main antagonists could be a group of rogue ninjas who are after the secrets of the Uzumaki clan. Since Naruto is Mito's brother, they might target him to get to those secrets.
Another possibility is that there are some sort of ancient evil forces. Maybe there are dark entities that were sealed away long ago and Mito's connection to the Nine - Tails somehow awakens them. These forces could be more powerful than the normal ninja threats and would pose a great challenge to Mito and the Hidden Leaf Village.
Well, obviously Naruto and Mito Uzumaki are the main characters. Naruto, the protagonist of the Naruto series, is a powerful ninja with the Nine - Tails sealed within him. Mito Uzumaki was the first jinchuriki of the Nine - Tails in Konoha. In fanfiction, they are often the central focus, whether it's about their relationship, their powers, or their roles in the history of the ninja world.
Since it's about Uzumaki Mito, she is likely one of the main characters. There might also be other characters from the Naruto universe like Hashirama Senju, as he was related to Mito. Maybe some of the early villagers of Konoha could be in it too.
It could be a group of rogue ninja who are after the Uzumaki's powerful sealing jutsu. They see it as a way to gain unlimited power and rule the ninja world, so they target the Uzumaki clan, which makes Naruto their main enemy as he stands in their way.
The main antagonists could be some of the conservative elders in the Hidden Leaf Village. They banished Naruto in the first place and would see his rebuilding of the Uzumaki clan as a threat to their power. They might try to undermine his efforts by spreading false rumors about him and his new clan.
Perhaps an old enemy of the Uzumaki clan, long thought to be defeated, resurfaces. They see Naruto as a threat because of his position as the heir and aim to eliminate him before he can fully embrace his Uzumaki heritage and power. This could be someone with a vendetta against the Uzumaki for past events, like a clan that was defeated by the Uzumaki in the past and now wants revenge.
It could be a group of rogue ninjas from Naruto's world who have found a way to cross over to Korra's world and cause chaos. They might want to steal the bending abilities for their own evil purposes.
One possible main antagonist could be a dark wizard or sorcerer who wants to harness the combined powers of Naruto and Artemis for his own evil purposes. He might see Naruto as a key to getting closer to Artemis and stealing her powers. Another could be a rogue ninja from Naruto's world who has turned against him due to jealousy of his new connection to Artemis.
It could be a creature from Renamon's world that is jealous of the bond between Naruto and his brother. This creature might see their connection as a threat to its own power or status in Renamon's world. So it sets out to break their bond and cause chaos between the two worlds.
One possible plot could be Naruto discovering his connection to Mito Uzumaki early on. This could lead to him having an easier time controlling the Nine - Tails' chakra as Mito was also a Jinchuriki. He might inherit some of her unique sealing techniques and use them to protect the village in new ways.