Perhaps a powerful ninja who doesn't like the idea of an outsider like Miku in their world. This ninja might see Miku as a threat to the traditional ninja way of life and decides to get rid of her. They could use their knowledge of the ninja arts and the terrain to set up traps and attacks against Miku and her new - found friends in the Naruto world.
It could be someone from Miku's world who follows her into the Naruto universe and has evil intentions. Maybe a jealous rival who wants to stop Miku from becoming popular in the new world.
There could be a dark force that is awakened by Miku's arrival in the Naruto universe. This dark force could be something that has been sleeping for a long time and Miku's unique energy stirs it up. It then becomes the main antagonist, trying to destroy both Miku and the Naruto world. It might have the ability to corrupt the minds of the ninja and turn them against Miku.
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.
It could be a rogue ninja who has mastered parkour to an extreme level. He uses his skills to steal important ninja artifacts and Naruto has to stop him. This antagonist would be very fast and agile, making it difficult for Naruto to catch him using normal ninja techniques.
Madara could still be the main antagonist even in a 'naruto bankai fanfic'. He senses Naruto's new power and realizes it could be a threat to his plans of world domination. He adapts his strategies and attacks Naruto with all his might, trying to prevent Naruto from fully mastering and using his Bankai - inspired power to its fullest potential.
A powerful and corrupt ninja from another village could be the main antagonist. He hears about the unique knives in Naruto's village and decides to steal them to increase his own power and the dominance of his village. He would stop at nothing to get his hands on these knives, even if it means starting a war between the villages.
A mysterious figure within Konoha who has a hidden agenda. This person doesn't like the idea of Naruto breaking the norms and wearing a dress. They secretly manipulate events to make Naruto's life difficult while he's in the dress. For example, they might arrange for Naruto to be in situations where his dress - wearing causes maximum embarrassment, all in an attempt to make him conform to the traditional ways.
It could be Orochimaru. He has always been interested in the power of the dead and bringing back the strong. He might have found a way to reanimate Naruto for his own evil purposes, like using Naruto's power to take over the ninja world.
A group of ninja who oppose the new order of the Naruto Empire could be the main antagonists. They might believe that the empire has become too controlling or has strayed from the original values of the ninja world. They could use guerrilla tactics and create internal unrest within the empire to try and bring it down.
It could be a rogue ninja who wants to use the mummy's power for evil. He might have discovered some ancient scrolls that told him about the mummy's potential and is now trying to awaken it fully and control it to take over the ninja world.
A rogue ninja from another village could be the main antagonist. Maybe a ninja from the Hidden Mist Village who has a personal grudge against Konoha and sees Naruto as the symbol of Konoha's strength. So, he devises a complex plan to take down Naruto. This ninja could have some unique and deadly jutsu that Naruto has never faced before, which ultimately leads to his downfall.