Perhaps an ancient evil spirit that was sealed away long ago and is now awakened. It senses the power of the fem Kyuubi and Naruto's growing strength. This spirit wants to absorb their power to regain its full form and wreak havoc on the ninja world. So it becomes the main antagonist, trying to separate Naruto and the fem Kyuubi so it can defeat them one by one.
Maybe a dark organization that has been researching the tailed beasts. They want to use the fem Kyuubi and Naruto's connection to unlock some sort of ultimate weapon. Their leader would be the main antagonist, constantly sending his minions to disrupt Naruto and the fem Kyuubi's relationship and stop them from getting stronger.
It could be an evil ninja who wants to capture the fem Kyuubi for her power. He might see the unique bond between Naruto and the fem Kyuubi as a threat to his plans of world domination.
Obviously, the fem Kyuubi herself could be the main antagonist. Since she is the one manipulating Naruto, her actions are causing problems and driving the conflict in the story.
It could be other powerful ninja clans who see the fem Kyuubi's possessive behavior towards Naruto as a threat to their own power and influence. They might try to separate them.
It could be Orochimaru. He might want to use Ino's connection with the Kyuubi to his own advantage. Maybe he plans to extract the Kyuubi's power through Ino's mental link with it.
In this fanfiction, perhaps Naruto meets the fem Kyuubi in a different dimension. The fem Kyuubi might be a more gentle and intelligent version compared to the traditional Kyuubi. She could teach Naruto some ancient ninja techniques that were lost long ago. They might also form an alliance to fight against a new common enemy that is threatening the Hidden Leaf Village.
It could be an ancient shinobi who once tried to control the Kyuubi but was sealed away. Now, with Naruto as the new host, he sees an opportunity to take over the Kyuubi's power again.
It could be a rogue ninja who has a vendetta against the Hidden Leaf Village and specifically targets Naruto and Fem Katsuyu because of their unique partnership. This ninja might have some dark jutsu that can counter Fem Katsuyu's abilities.
Madara Uchiha could also be a main antagonist in this fanfiction. He has grand plans for the ninja world and the released Kyuubi could be a key part of his scheme. Since Naruto is dead and can't oppose him, he might try to use the Kyuubi to reshape the world according to his vision. He has the power and the ambition to be a major threat in this situation.
It could be Orochimaru. He's always been interested in power and the secrets of the Kyuubi. With Naruto releasing the Kyuubi fuuinjutsu, Orochimaru might see this as an opportunity to either steal Naruto's power or use him for his own evil experiments.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
It could be someone who wants to steal Samehada for its power. Maybe a rogue ninja who has heard of Samehada's ability to absorb chakra and plans to use it to take over the ninja world.