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.
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.
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 someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
It could be another dark mage who sees the potential in baby Natsu and wants to use him for evil purposes. This mage might view Zeref as an obstacle in getting to Natsu.
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.
It could be Orochimaru. He might see the baby versions of Team 7 as perfect subjects for his experiments. He could try to kidnap them to use their unique chakra or potential for his own dark purposes.
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.
It could be an old vampire enemy of Damon's. Maybe someone from his past who has a vendetta against him and sees the baby as a way to get revenge. This antagonist could try to kidnap the baby or cause trouble in their lives.