Maybe it's another Saiyan who doesn't approve of Bulma and Vegito's relationship. This Saiyan could be causing trouble for them, and Bulma might feel like she has to give up on Vegito to stop the conflict. For example, a traditional - minded Saiyan who thinks that a human and a fused Saiyan like Vegito shouldn't be together.
It could be Frieza. He might be jealous of Vegito's power and decides to target Bulma to get to Vegito. His actions could make Bulma realize the danger she's in because of her association with Vegito, leading her to give up on him.
Well, it could be that Bulma realizes that the relationship with Vegito is just too complicated or dangerous. Maybe she decides that she can't handle the chaos that often surrounds Vegito, like all the battles and threats that come with being associated with him.
Maybe it's because Bulma has her own established character traits and relationships in the original story. She might not fit well into the scenarios often presented in Vegito fanfic. Also, her character is more focused on other aspects like her scientific work and family in the canon, so fanfic ideas involving her in a Vegito - related context could seem out of place to her character.
Frieza could be a great antagonist. He has a history with Broly and would be interested in Bulma's technology. He might see Broly's new alliance with Bulma as a threat and try to break it up. Frieza could also want to use Bulma to create powerful weapons or devices for his own evil purposes.
It could be Frieza. He might be interested in Bulma's technology for his own evil purposes and sees Chichi as a threat because of her connection to the powerful Z - Fighters. So he tries to stop their partnership and steal Bulma's inventions.
One reason could be that the fanfic might distort her character. Bulma is a smart scientist, and if the Vegito fanfic makes her act in a way that's not true to her intelligent and rational self, she would seem to reject it. For instance, if the fanfic has her being overly emotional or doing things that are completely against her scientific nature just to fit into a Vegito - centered plot.
It could be the Hidden Leaf Village's elders. If they are shown to be manipulative and using Naruto for their own political gains, and Naruto eventually finds out, they would become the main antagonists. He might see their actions as the root of all his problems and turn his hatred towards them for exploiting him.
To write a Bulma leaves Vegito fanfic, start with character development. Understand Bulma's and Vegito's personalities well. Maybe Bulma has grown tired of Vegito's constant battles and wants a more peaceful life. Then, build a conflict that leads to her leaving. As you write, use vivid descriptions to bring the story to life. You can include flashbacks to show the history of their relationship. And make sure to have a resolution at the end, whether it's a reconciliation or a final goodbye.
It could be an evil wind - based ninja who has been misusing the power of the wind. Naruto gives his body to the wind to combat this antagonist directly on its own element's territory.
Kabuto could be an antagonist as well. He is a power - hungry character. If Naruto is trying to bring positive change to the Akatsuki, Kabuto's thirst for power and his underhanded tactics could put him in direct conflict with Naruto, as he might see Naruto as a threat to his own plans within the Akatsuki.
Another possibility is that the main antagonist could be some sort of ancient evil that is awakened by the events in the fanfic. Dumbledore might have given Snape to Harry because he sensed this new threat. This ancient evil could have powers that are unknown to the modern wizarding world and it would be up to Harry and Snape to figure out how to defeat it.