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.
It could be Orochimaru. He might be interested in the baby for some dark experiment, thinking the baby has unique chakra or abilities that he can use for his own gain. He would stop at nothing to get his hands on the baby, which would put Kakashi and Sakura in a tough situation to protect it.
It could be a rogue ninja from a rival village. This ninja has a personal vendetta against Konoha and specifically targets Team 10 because of Naruto's presence. He might be jealous of Naruto's growing power and fame and wants to prove himself by defeating the team.
Maybe an organization that wants to use her unique abilities. If she has inherited some special power from Kakashi or has her own distinct skills, an evil organization could try to capture her and force her to work for them. They would be the main obstacle she has to face in the story.
Perhaps an old enemy of Naruto's who resurfaces and decides to target his family. This could be someone who was defeated by Naruto long ago but has now grown stronger and wants to cause harm to his loved ones. They might also see Kakashi as a threat in protecting the family.
It could be Orochimaru. He might be interested in the unborn child for some dark experiment, thinking that the child of Kakashi and Rin could possess some unique abilities. He could send his minions to spy on them or even try to kidnap Rin.
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.
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.
Perhaps an old enemy of one of the members of Team 9 shows up. Since Naruto has joined the team, they might see it as an opportunity to get revenge. This antagonist could be someone who was once defeated by the member's family and now wants to prove themselves. They would be very cunning and use their knowledge of the team member's past to try and divide the team.
It could be Danzo. He's always been a bit of a shadowy figure in the Naruto series. Maybe he sees Naruto as a threat to his power and influence in the village and manipulates the situation so that Team 7 has to abandon him. He would be a great main antagonist as he has the resources and the motives to cause such a rift in Team 7.
It could be an evil ninja who wants to stop Kakashi from meeting his mother. This ninja might be from a rival village and fears that Kakashi will gain some powerful knowledge or ability from his mother that could be a threat to their plans.