A lesser - known but interesting antagonist could be a rogue ninja who blames the Fourth Hokage (Naruto's father) for something. When he finds out Naruto is the Fourth's son, he decides to take revenge on the baby, thinking it would be a way to get back at the late Hokage.
Danzo could be a great antagonist even when Naruto is a baby. He might see Naruto as a threat to his plans for Konoha's future and try to get rid of him secretly while making it look like an accident.
It could be Orochimaru. Since Naruto was a potential threat to his plans in the original story, if Naruto died as a baby, Orochimaru might be able to carry out his experiments and schemes more freely without having to worry about Naruto interfering in the future.
It could be Orochimaru. Imagine Orochimaru discovers baby Naruto's time - traveling ability and wants to use it for his own evil purposes. He might try to manipulate baby Naruto to change the timeline in a way that benefits him, like making it easier for him to gain more power or revive his dead comrades.
Another vampire family that is jealous of the Mikaelson's power and influence. They see the baby as a threat to their future plans. They might try to kidnap the baby and use it as a bargaining chip to gain more power in the vampire world. They would be constantly plotting against the Mikaelsons to get their hands on the baby.
It could be Danzo. He was always power - hungry and had his own ideas about how the village should be run. He might see Naruto as a threat to his plans, so he locks Naruto away as a baby. He wants to control the village without the interference of the jinchuriki's power.
A powerful dark wizard could be a great antagonist. He might want to use the Scarlet Baby's unique energy for his dark magic. He could send his minions, like flying monkeys or shadow serpents, to capture the baby.
A human noble who doesn't approve of Ariel and Eric's union and especially doesn't like the idea of a half - human, half - mermaid baby. This noble could try to create problems for the family, like spreading false rumors or trying to get the baby separated from its parents. Another possibility is a sea monster that has been awakened by the birth of the baby, seeing it as an intrusion in its territory and trying to harm the baby and its parents.
An overzealous social worker who believes that Rizzoli and Isles are not fit to take care of the baby due to their dangerous jobs. This social worker could constantly be trying to take the baby away from them, creating a lot of conflict and drama in the fanfiction. Rizzoli and Isles would then have to prove that they can be great parents despite their demanding careers.
It could be an old enemy from their past, like a vengeful monster. Maybe a cyclops that they once defeated and now it wants to take revenge on them through their baby.
A group of rebels who have different ideas about how to handle the situation of the baby could also be the antagonists. They might think that Effie and Haymitch are too soft or too Capitol - influenced in their parenting of the baby. So they try to take the baby from them to raise it in their own way, believing it will be better for the future of the rebellion and the new society they are trying to build.
A sly fox from an old - fashioned fox gang could be the main antagonist. This fox might see the baby fox as a threat to their way of life or might want to use the baby fox's innocence for their own devious plans.