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.
Well, it could be about Naruto having a secret brother who is related to Gliats in some way. Maybe they team up to fight a common enemy, or there could be a story of family secrets and revelations.
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.
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.
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.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.