One popular 'antagonist naruto si fanfic' is 'The Dark Shinobi'. It has an interesting take on a self - inserted character as an antagonist. The story is full of action and unique plot twists that deviate from the original Naruto storyline in a captivating way.
First, you need to have a clear concept of your self - inserted antagonist. Decide on their personality, goals, and backstory. For example, if they are a power - hungry shinobi, think about what drove them to that. Then, familiarize yourself with the Naruto world's rules, clans, and jutsu. This will help you create a more believable story.
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.
Perhaps an evil organization that wants to harness the power of both Naruto and Nero. They might see Naruto's chakra and Nero's Devil Bringer as the keys to ultimate power. This organization could be led by a powerful sorcerer who can manipulate dark magic and has minions from both worlds at his disposal.
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.