It could be that an old enemy of Stefan's family decides to target Bella as a way to get back at Stefan. This enemy might be another vampire clan or a supernatural being with a long - standing grudge. They would do everything in their power to disrupt the relationship between Bella and Stefan, causing all sorts of problems and conflicts for the two of them in the fanfiction.
Often, in these fanfictions, other vampires can be the main antagonists. For example, a jealous vampire who wants Stefan for herself might see Bella as a threat and try to drive them apart.
It could be other vampires who are jealous of their unique relationship. Maybe there are some traditionalist vampires who don't accept this new kind of mating bond among them.
In some fanfictions, it could be the Volturi. They might see Bella and Alec's relationship as a threat to their power or their rules about vampire relationships. They could try to break them apart or manipulate the situation to their advantage.
The Volturi could be main antagonists. Since they have strict rules about vampires and humans, they might see Bella and Jasper's relationship as a threat to their order.
In this fanfiction, there might be some werewolves who view the baby as an abomination since it's part vampire. They could try to harm the baby, which would put Bella and Stefan in a difficult position to defend their child.
Some fanfictions might have a plot where Bella and Stefan try to integrate their lives. Since they come from different fictional universes (Twilight and The Vampire Diaries), they could face difficulties in getting along with each other's friends and families. There could be a lot of drama as Bella tries to understand Stefan's past with Katherine and other vampires, and Stefan tries to understand Bella's connection with Edward. This exploration of their relationship in the context of their complex pasts can make for a really engaging plot.
In some fanfictions, Voldemort or his remaining Death Eaters could still be the main antagonists. They might target Harry and Neville specifically because they see them as a threat to their plans of taking over the wizarding world again.
It could be a rogue Death Eater who escaped the clutches of justice after Voldemort's fall. This Death Eater might be seeking revenge on Harry and decides to target Bill as well since he's Harry's mate.
There could be a new vampire hunter in town. This hunter could target Stefan and Elena because of their relationship. He might believe that their union will create a more powerful vampire line and wants to stop it before it's too late.
The Mikaelson family, especially Klaus, could be antagonists. He might see the pregnancy as a threat to his family's power or reputation. He could try to stop Stefan and Rebekah from being together and having the baby.