Another possibility is a powerful dark wizard - like figure who has a vendetta against Mikoto's family. When they find out about the apprentice, they target the apprentice to get to Mikoto, thinking that by harming the apprentice, they can break Mikoto's spirit.
It could be a rogue ninja from a rival village who is after the apprentice's special abilities. This rogue ninja might see the apprentice as a threat or a tool to achieve their own evil goals.
One possible plot could be that the apprentice has a unique jutsu that Mikoto wants to help develop. So, they go on various missions together to test and refine it, facing different enemies along the way.
It could be Orochimaru. Since Anko has a history with Orochimaru, and Nariko being Anko's apprentice, Orochimaru might see Nariko as a threat or a tool to get to Anko. He could try to manipulate Nariko into doing his bidding or try to steal her newfound skills.
The apprentice could be a new genin who shows great potential in the field of intelligence gathering. Maybe someone with a sharp mind and an ability to stay calm under pressure, like Shikamaru. He has the intelligence and strategic thinking that would make him a good candidate for Ibiki's apprentice.
It could be an original character created specifically for the fanfic. Maybe a young ninja with a unique kekkei genkai that Kakashi sees potential in.
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.