Maybe there are some secret organizations that want to study the baby because it's a hybrid of Ben and Gwen's powers. These organizations might not have evil intentions at first, but their methods of trying to get the baby could make them antagonists as they go against Ben and Gwen's wishes to protect their child.
The antagonists could be forces of dark magic. They might sense the power within the baby and want to either corrupt it or use it for their own evil purposes. For example, there could be a sorcerer who wants to steal the baby and raise it to be his minion. Also, some neighboring kingdoms that see Camelot's new heir as a future threat might send spies or assassins to target the baby.
Well, one possibility could be that the baby inherits some of Ben's alien powers in a really unique way. Maybe it's not as straightforward as having the Omnitrix, but has some latent abilities that start to show as it grows. And Gwen could be teaching the baby how to control any magical tendencies it might have, since she has her own magic skills.
Well, it could be about how Ben and Gwen adjust to their new roles as parents. Maybe they face challenges like protecting the baby from villains who might want to use the baby's special powers (assuming in the fanfic world the baby has some).
The baby could have Ben's adventurous spirit. Since Ben is always eager to jump into action and explore new things, the baby might show signs of that same enthusiasm from a very young age. Maybe it would constantly be trying to reach for Ben's Omnitrix - like a shiny object that fascinates it.
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.
The Volturi could be antagonists. In the Twilight universe, they are the powerful vampire coven that enforces vampire laws. They might see the baby as a threat to their power or a violation of their rules. They could try to eliminate the baby or control Bella, Edward, and their family.
One possible antagonist could be an evil scientist who wants to study the baby's unique genetic makeup. Since Shadow and Blaze are both special characters, their baby would likely have an interesting genetic combination that the scientist could use for his own malicious purposes.
Maybe an old acquaintance from their past who has a grudge against them. This person could spread rumors about them being unfit parents just because they are in a same - sex relationship. And that would create a lot of problems for Emily and Alison as they prepare for the baby.
It could be Bowser. He might see the new baby as a way to get to Daisy and Luigi. He could try to kidnap the baby to use as leverage against them.
It could be some of the traditional antagonists from the original story, like the Volturi. They might see the baby as a threat to their power or the order they've established in the vampire world.