Well, some other shinobi from rival villages might be antagonists. They could see the potential relationship between Naruto and Fem Sasuke as a threat to their own village's interests. So, they might try to create problems between them. For example, they could spread false rumors about Naruto to Fem Sasuke, making her doubt him and break his heart. And sometimes, Fem Sasuke's own family members or clan elders, if they have different plans for her future that don't include Naruto, could act as antagonists in the story.
Orochimaru could be a likely antagonist. In the original Naruto story, he had a strong influence on Sasuke. In the fanfiction with Fem Sasuke, he might manipulate her to turn away from Naruto, causing Naruto's heartbreak. Another could be Danzo. His underhanded and power - hungry ways might lead him to interfere in the relationship between Naruto and Fem Sasuke, perhaps by setting up situations that make Fem Sasuke distrust Naruto.
It's possible that some of Fem Sasuke's own inner demons could be considered antagonists in a way. For example, her thirst for revenge or her insecurities. These things could cause her to act in ways that hurt Naruto and lead to his heartbreak. Also, in some fanfictions, there might be a new, original character created specifically to cause trouble between Naruto and Fem Sasuke. This character could be jealous of their relationship or have their own ulterior motives.
It could be Orochimaru. He might see the potential in the relationship between Naruto and female Kiba as a threat to his plans. Maybe he wants to use their connection to his advantage or simply disrupt it to create chaos in the village.
Well, in this kind of fanfiction, a frequent theme is the struggle between duty and love. Fem Sasuke might feel that her duty to her clan or village conflicts with her feelings for Naruto. This inner conflict can lead to her pushing Naruto away, thus breaking his heart. And sometimes, the theme of jealousy pops up. If there are other characters interested in Naruto or Fem Sasuke, it can create a lot of drama and heartbreak for the main characters.
In some fanfictions, a new character could be created as the main antagonist. This character might be jealous of Naruto and female Sasuke's growing relationship and power. They try to create rifts between them and stop them from achieving their goals.
The Akatsuki could be likely antagonists. They are always interested in powerful ninja like Naruto. They might use some forbidden jutsu to control Naruto to further their goals of collecting the tailed beasts. Another possibility is Orochimaru. He is always looking for ways to gain power and Naruto's power would be very appealing. He could try to control Naruto to use him in his experiments or to fight his enemies for him.
The Akatsuki could be a likely antagonist. Since they were always a threat in the original series, in a Konoha - destroyed scenario, they might try to capitalize on the chaos and further their own goals.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
Another character could be Kakashi. Maybe he has to make a tough decision that goes against Fem Naruto's wishes. For example, not allowing her to go on a dangerous mission she really wants to. This could make Fem Naruto feel betrayed and heartbroken, as Kakashi is a respected figure in her life.
Well, it could be Orochimaru. He was always up to no good and had an interest in powerful ninja. He might target Naruto and Temari to either steal their powers or use them for his evil experiments, which would surely lead to them getting hurt.
One possible antagonist could be a rogue ninja from another village. They might target Tenten for her unique weapon - handling skills, thinking they can use her to create powerful weapons for themselves. Naruto would then have to face this ninja to save Tenten.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.