Maybe it's a member of a new and mysterious organization. They want to create chaos among the villages by making Naruto and Mei distrust each other during the interrogation. Their goal could be to start a war between the Hidden Leaf and the Hidden Mist so they can profit from the chaos.
There's also a chance that the antagonist is an old enemy of Mei's who has a grudge against her. They use the situation of the interrogation to try and frame Mei for something she didn't do, and Naruto has to figure out the truth while dealing with this person's schemes.
Well, it could be about Naruto interrogating Mei to find out some secrets related to the Hidden Mist Village. Maybe there are some political intrigues or threats to the Allied Shinobi Forces that Naruto suspects Mei knows about.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
It could be an organization similar to the Akatsuki, but with a different goal. Instead of collecting tailed beasts, they are focused on conquering villages. Their army would be made up of powerful and diverse fighters, and Naruto would have to face their leader, who has some sort of special power or ability that makes them a formidable foe.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
It could be a new character, perhaps someone from a far - off land who has a grudge against Naruto's future self for some reason. This character might be extremely powerful and has plans to destroy everything Naruto holds dear. When Naruto sees this future, he has to find a way to stop this new threat before it even begins to form.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.