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.
Maybe an ancient evil spirit that has been awakened due to some imbalance in the world. This spirit could be powerful enough to pose a threat to both Naruto and Korra. It might try to turn them against each other or simply destroy them to gain complete control over the two worlds. In addition, there could be some corrupt politicians in Korra's world who see Naruto as a threat and try to get rid of him while he's trying to help Korra maintain peace.
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.
Well, it could be certain political rivals. Maybe there are those who fear that the child of Korra and Iroh will have a strong claim to leadership or influence in the future. So, they become the antagonists, trying to create problems for the couple during the pregnancy. It could also be some dark spirits or entities that sense the special nature of the unborn child and want to prevent it from being born, seeing it as a potential obstacle to their own dark purposes.
Maybe there are some dark forces from the land of Gliats that don't want Naruto's brother to have a connection with Konoha. So they send their agents to cause trouble and try to sever the new - found relationship between Naruto and his brother.
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.
It could be a group of rogue ninjas from a rival village. They might see the little brother as a way to get to Naruto or the Hidden Leaf Village. They could try to kidnap him to use as a bargaining chip or to extract information about the village's defenses.
One possible antagonist could be Orochimaru. He is always interested in obtaining powerful individuals or unique abilities. Koneko's potential might draw his attention, and Naruto would have to protect her from him.
One possible main antagonist could be a power - hungry ninja who wants to use Naruto's connection to the Sage of Six Paths for their own evil purposes. They might try to kidnap Naruto to extract the secrets from him.
Well, it could be about Naruto being Korra's brother and them having to face some common enemy together. Maybe they discover some ancient power that only they, as siblings in this fanfic, can control.
The main antagonists could be some of the more traditional and power - hungry gods. For example, Hera might see Percy as a threat to the order she has maintained for so long. She could try to undermine him at every turn, fearing that his new ideas and his relation to Zeus will disrupt her plans. Another antagonist could be Ares, who might be jealous of Percy's potential power and influence over the other gods and demigods.