Perhaps an organization that wants to mass - produce the Hiraishin Kunai and use them to take over the ninja world. Their leader could be a power - hungry figure who sees the kunai as the key to ultimate domination.
A dark spirit that has been trapped within a Hiraishin Kunai for centuries. When the kunai is unearthed, the spirit is released and starts causing chaos in the ninja world. It would be a powerful and mysterious antagonist that Naruto and his allies would have to figure out how to defeat.
It could be a rogue ninja who has a deep understanding of the Hiraishin Kunai's power and wants to use it for evil. Maybe he was once a student of Minato but turned bad.
It could be an unknown enemy who is manipulating Dark Naruto's use of Ino's kunai. This enemy might have a vendetta against the Hidden Leaf and sees Dark Naruto as a tool. They secretly guide him in misusing the kunai to achieve their own evil goals.
It could be a rogue ninja who was once a student of the Hiraishin master but turned evil. They might have a twisted view of the technique and use it for their own selfish and harmful purposes, like stealing important artifacts from different villages.
One idea could be a story where a young ninja discovers an ancient Hiraishin Kunai and tries to master its power. He could face challenges like rival ninjas trying to steal it.
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.
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.
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.