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.
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 new villains from the multiverse. As Loki and Peter start exploring different realms together, they could encounter beings who want to use Peter's powers for their own evil plans. These villains might be powerful magic - users or creatures that are not from Earth and have different motives and abilities.
Well, perhaps Loki discovers an orphaned baby in a dangerous situation. He decides to take the baby in out of a sense of pity or a newfound sense of responsibility. Maybe he uses his magic to protect the baby from various threats in the Nine Realms.
The Frost Giants could be a main antagonist. Since Loki has a history with them, they might see his baby daughter as a way to get revenge on Loki or gain some advantage in the power struggle with Asgard. They could try to kidnap her to use her as a bargaining chip.
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.
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.
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.
The Death Eaters could still be the main antagonists. They might see Fenrir's new alliance with Harry as a threat. Since they once used Fenrir for their dark deeds, they don't want him to turn good and expose their secrets.