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.
The main antagonist could be the fem Kyuubi. Think about it. She's the one using Naruto for her own ends. She might be trying to break free from some sort of seal or gain more power through Naruto, and in the process, she's making Naruto act against his own nature. So, she's the root of all the trouble in this fanfiction.
One possible plot could be that the female Kyuubi uses her charm and power to manipulate Naruto into making hasty decisions. For example, she might convince him to take on dangerous enemies alone without proper preparation. This could lead to Naruto facing challenges that test his limits in new ways.
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.
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 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.
It could be another powerful entity that is secretly manipulating the situation. Maybe there is a dark shinobi or a hidden organization that wants to see the Kyuubi and Naruto at odds. They could be the ones who set in motion the events that lead to Naruto scaring the Kyuubi. For example, they might have given Naruto a false power or false information that is causing the Kyuubi to be scared, all in an attempt to further their own evil plans. This entity would then be the main antagonist as they are the real source of the conflict.
Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
It could be an ancient evil spirit that was sealed away by Fem Hashirama in the past. Now that she has resurfaced in the Naruto - era, the spirit is also awakened. This spirit wants to destroy the world that Fem Hashirama once protected and Naruto, being the hero of his time, stands in its way along with Fem Hashirama.