Maybe Orochimaru could be the antagonist. He hears about Naruto's encounter with Yagura and wants to use their connection for his own evil experiments. He might try to capture Yagura again (if he was once under Orochimaru's control) or manipulate Naruto into doing something that would harm Yagura and the relationship between the two villages.
The antagonist could be a powerful dark spirit that has been possessing Yagura and making him act in a negative way. Even after Naruto meets Yagura, this dark spirit tries to regain control and cause destruction. Naruto has to not only fight against the physical manifestations of the spirit but also figure out a way to exorcise it completely from Yagura.
The plot could involve Yagura being freed from the control of the evil forces that once manipulated him. Naruto, being the hero he is, senses something strange about Yagura. He then uses his shadow clones to investigate. When he discovers the truth, he uses his chakra to break the hold on Yagura. After that, they form an alliance to help the Hidden Mist Village recover from the damages caused by Yagura's previous actions under control.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
It could be a rogue ninja who is after Sakumo's hidden techniques. Since Naruto meets Sakumo, this rogue ninja sees Naruto as an obstacle and tries to eliminate him. This antagonist might have a grudge against the Hatake clan and wants to use Sakumo's secrets for his own evil purposes.
It could be someone who wants to steal Samehada for its power. Maybe a rogue ninja who has heard of Samehada's ability to absorb chakra and plans to use it to take over the ninja world.
It could be a powerful alchemist who has gone rogue and wants to use Naruto's chakra for some dark alchemy purpose.
It could be an evil ninja who wants to capture the fem Kyuubi for her power. He might see the unique bond between Naruto and the fem Kyuubi as a threat to his plans of world domination.
It could be that Yagura had some secret plans that would endanger the balance among the ninja villages. Naruto, having a strong sense of protecting peace, discovers these plans and decides that eliminating Yagura is necessary. For example, if Yagura was planning to use a powerful and dangerous jutsu that could destroy multiple villages, Naruto would act to prevent it even if it means killing him.
It could be someone who doesn't want Naruto and his sister to unite. Maybe a rogue ninja who fears their combined power. He might try to drive a wedge between them by spreading false rumors or causing misunderstandings.
It could be an evil shinobi who wants to disrupt the meeting between Naruto and Kushina. Maybe they know that Kushina has some special knowledge or power that she could pass on to Naruto, and they don't want that to happen.
It could be a rogue Sound ninja who has his own agenda. Maybe he wants to start a war between Konoha and the Sound Village to gain power in the chaos. He would see Naruto as a threat to his plans and try to eliminate him.