Well, there could be a new antagonist created specifically for this fanfiction. Maybe a powerful sorcerer who wants to use the power of their union for his own evil purposes. He could try to manipulate events so that Naruto and Koneko turn against each other. Additionally, some of the conservative elements in both of their worlds who don't approve of inter - world relationships could also act as antagonists, trying to stop their marriage through political or social means.
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.
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.
Perhaps there are other divine beings who are jealous of the cat goddess's relationship with Naruto. They could see Naruto as an unworthy mortal and try to disrupt their marriage. These divine antagonists could use their powers to create all sorts of troubles for Naruto and the cat goddess, like causing natural disasters or sending powerful minions to attack them.
Well, one possibility could be that Naruto somehow enters the world where Koneko exists. Maybe there's a strange jutsu gone wrong that transports him. They meet, and Naruto's kind and determined nature attracts Koneko. Eventually, they fall in love and get married. Naruto might introduce Koneko to his friends in Konoha, and she could share her unique skills with them.
The Malfoy family could be antagonists. They might see Harry as an enemy still and not want Daphne, a pure - blood, to marry a half - blood like Harry. They could try to create problems between the two, spreading rumors or trying to sabotage their relationship.
Maybe an old enemy of Natsu's resurfaces. This enemy is jealous of Natsu's newfound happiness with Cana and tries to take Cana hostage to force Natsu to fight him. This would create a major conflict in the fanfiction.
It could be Sasuke's sister, if there was one in the fanfiction world. She might share some of Sasuke's traits but also have her own unique personality that attracts Naruto.
Another possibility is Sakura. Although she has feelings for Sasuke in the original, in this fanfiction, the story could be rewritten so that she realizes her true connection with Naruto and they end up getting married at 12. Their dynamic would be quite different from the original, with Naruto having to prove himself in a new way to Sakura.
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.
One potential antagonist could be a group of rogue ninjas who see Sarada's pregnancy as a sign of weakness in the village. They might try to target her to cause chaos. Another could be a jealous rival who doesn't like the attention Sarada is getting due to her pregnancy and her connection to Naruto.
It could be Orochimaru. He might be interested in the baby's unique genetic makeup, thinking he can use it to create more powerful experiments. He has always been obsessed with power and the baby's combination of Naruto and Temari's abilities would be very appealing to him.