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.
The Akatsuki could also be antagonists. They are on a mission to collect the tailed beasts, and if Koneko has some special power related to the ninja world, they might target her. Naruto, being the older brother, would fight against them to keep her safe.
There could be a new group of rogue ninjas. They might envy Koneko's growing power under Naruto's tutelage. So they try to disrupt their training and cause harm to Koneko. Naruto would then have to use all his skills and experience to fend off these new threats.
The plot might involve Naruto helping Koneko to discover her own power. Since Naruto has been through so much in terms of self - discovery, he could guide her. For example, he might take her on adventures where she has to face her fears, just like he did in his journey to become a great ninja.
In this fanfiction, the antagonists might be a group from Koneko's world who oppose her relationship with an outsider like Naruto. They might fear that Naruto will bring chaos or change their traditional ways. They could try to separate them by any means necessary, including using their own unique powers against Naruto. Also, some of the rogue ninja from Naruto's world who are jealous of Naruto's new relationship could also cause trouble.
There could also be other characters from the Naruto series like Sasuke, Sakura, and Kakashi. They might interact with Naruto and Koneko in different ways. For instance, Sasuke could be initially suspicious of Koneko but later become her ally. Sakura could help Koneko with her medical ninjutsu training if Koneko shows an interest. And Kakashi could be the one to guide them in some difficult missions or training sessions.
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.
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.
In the fanfiction, it might also explore their family background. Since Naruto has always been alone in the original story, having a sister like Koneko could change his view on family. They could uncover secrets about their family together, like where their parents came from or if there are any special inheritances that come with their family line.