Voldemort or his remaining Death Eaters are often common antagonists. Even after his defeat in the original story, in dark fanfiction, they could come back in some form to target Harry and Ginny. For example, a Death Eater who escaped justice might seek revenge on Harry by harming Ginny.
Dark magical creatures can also serve as antagonists. For instance, a group of Dementors could be under the control of a dark force and target Harry and Ginny. Their presence could drain the happiness and hope from Ginny, making her more susceptible to dark influences, while Harry has to fight not only to save her but also to keep his own sanity in the face of such a soul - sucking threat.
In some cases, corrupt Ministry of Magic officials can be antagonists in 'Harry Potter Dark Business Fanfiction'. They could be involved in covering up or even profiting from the dark business. For example, they might turn a blind eye to the illegal trading of dangerous magical creatures in exchange for bribes. This would make them enemies of Harry Potter and those who strive for a just and clean wizarding world.
It could be Voldemort or his remaining Death Eaters. Since they have always been the main antagonists in the Harry Potter universe, in this fanfiction they might still be the ones causing the danger that leads to Harry's sacrifice for Ginny.
It could be the corrupt prison guards or wardens. They might be in league with dark forces outside Azkaban. They oppose Harry and Ginny because the couple is getting too close to uncovering their illegal activities within the prison, like smuggling dark artifacts or collaborating with Death Eaters.
Dark Matter is often a popular antagonist in dark Kirby fanfiction. It could be presented in a more powerful and uncontrollable form, corrupting everything it touches in Kirby's world. It might also have the ability to possess other characters, turning them against Kirby.
A new dark wizard could emerge in the wizarding world. This wizard might be jealous of Harry's fame and power and think that by getting to Lily, he can gain some sort of advantage. He could try to steal Lily's magic or use her to spread fear in the wizarding community.
The main antagonists could be the Death Eaters still loyal to Voldemort. They would be trying to undermine Harry and Ginny's efforts to protect Hogwarts and the wizarding world.
Perhaps the main antagonists are some of the old - fashioned wizarding council members who believe in arranged marriages for political stability. They force Harry into the marriage with Ginny without considering their feelings, and they would oppose any attempts by Harry and Ginny to break free from the forced union.
It could be a new dark wizard that they see in the future. Maybe someone who was overlooked during the fight against Voldemort but has been secretly gathering power.
Another possibility is a new dark wizard or witch who emerges and wants to prove themselves by taking on Harry and Ginny. This antagonist could be jealous of their fame and power and decides to target their DADA class to show that they are not as great as everyone thinks. They could try to undermine the students' confidence in Harry and Ginny's teaching.
The remaining Death Eaters could be the antagonists. Even though Voldemort is gone, there could be some who still hold a grudge against Harry and want to finish what their master started. They might track Harry and Ginny down as they run away, creating dangerous situations for the couple.