The main antagonist could also be a corrupt official within the Wave Country itself. After the events of the first mission, this official could have risen to power and now has plans to use his position to gain more control, even if it means going against Konoha. He could be secretly working with other villains or using his own resources to create problems for Naruto and his friends.
It might be a rogue ninja from the Wave. They could have a vendetta against Konoha and see Naruto as an easy target to frame and cause chaos between the two places.
Perhaps in this fanfiction, Naruto and his friends go back to the Wave Country for a follow - up mission. This time, they discover a new threat that is related to the power struggle they witnessed during the first mission. The group has to use their improved skills and teamwork to face this threat and protect the people of Wave.
A new organization that is bent on world domination could be the main antagonist. They set a trap during Naruto's mission. This organization might have access to some ancient and forbidden jutsu that they use against Naruto. They see Naruto as a major threat to their plans, so they target him specifically.
Maybe a rogue ninja who has made a pact with a dark wizard in Hogwarts could be the main antagonist. This ninja - turned - villain has combined his ninja techniques with dark magic and is causing havoc in Hogwarts. Naruto would be sent to stop him, but he'd face a tough challenge as this antagonist knows both the ways of the ninja and the secrets of Hogwarts magic.
In some fanfictions, Naruto becomes more confident after the Wave Mission. He realizes his own strength and the importance of his friends more deeply. For example, he might be more assertive in battles and decision - making.
It could be Danzo. He has always been suspicious of Naruto and might see this as an opportunity to get rid of him for good. He could spread false information to make the village turn against Naruto after the Pein attack.
It could be a power - hungry shinobi from another village. This shinobi sees Naruto's exile as an opportunity to gain more power and influence in the ninja world. He might try to hunt Naruto down to prove his own strength or to steal Naruto's secrets.
Perhaps a secret organization within the Hidden Leaf that wants to take over the village. They use Naruto as a scapegoat, getting him banished so they can carry out their evil plans without interference from Naruto. They would be the main antagonists as they are the ones behind the false accusations and the push for his banishment.
Perhaps a new, unknown force. With Naruto gone, a previously hidden group with a vendetta against the ninja villages could emerge. They might blame the villages for the destruction caused during the war and see Naruto's death as the perfect time to strike, when the villages are still recovering and vulnerable.
In some fanfictions, Sakura might become more confident after the Wave mission. She realizes the harshness of the ninja world and starts to train harder, not just relying on her teammates. For example, she could be seen spending more time in the hospital, learning advanced medical ninjutsu to be more useful in future battles.