The Ministry of Magic itself could be an antagonist. If they don't approve of Hermione's adoption due to her age or some bureaucratic reasons, they could try to take the baby away. They might think she's not fit to raise a child, which would create a lot of conflict in the story.
Maybe some dark elves or other villains from the Marvel universe. They could see the baby as a valuable asset or a threat, and try to harm the baby or use it against Loki. Since Loki is now responsible for the baby, he has to fend off these threats to keep the baby safe. For instance, the dark elves might think the baby has some special power and they want to harness it for their own evil purposes.
There could be a new dark wizard or witch emerging. This character could be jealous of Harry and Hermione's influence and see the baby as a way to get to them. They might try to harm the baby or turn it against Harry and Hermione, creating a lot of conflict and danger in the story.
Well, in this fanfiction, perhaps Hermione adopts a baby who has some sort of special magical ability. Maybe the baby is an orphan from a tragic event in the wizarding world. Hermione, with her kind heart and strong sense of justice, decides to take the baby in and raise it as her own. She would then face challenges like protecting the baby from dark forces who might want to use the baby's power for evil.
One possible antagonist could be Sabretooth. He might see Wolverine's newfound fatherly relationship with Peter as a weakness and try to use Peter to get to Wolverine. Sabretooth could be jealous of the bond Wolverine is forming and want to destroy it.
Well, in this fanfiction, it might start with Snape finding Hermione as a baby in a dangerous place like the Forbidden Forest. He adopts her because he sees her potential even as a baby. As she grows, he teaches her magic in his own strict way, but also forms a deep bond with her. This could lead to some interesting interactions with other Hogwarts faculty who are surprised by Snape's new role as a father figure.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
The main antagonists could be the traditional enemies of Camelot like Morgana. She might see Merlin's act of adopting Mordred as a threat to her plans. Also, some of the knights or nobles in Camelot who are superstitious and believe Mordred is a danger just because of the prophecies could be antagonists. They might try to separate Merlin and Mordred or even harm Mordred.
Voldemort's remaining followers could be antagonists. They might see the baby as a new threat or a potential weapon. They could try to kidnap the baby to use its power for their own dark purposes.
Perhaps there are some anti - Uchiha elements within the village that are not happy with Naruto adopting Sarada. They could try to undermine her training or create problems for Naruto and Sarada. They might spread false rumors or try to isolate Sarada from the rest of the village.