Another possibility is a new, mysterious organization that has emerged. They believe that the combination of Naruto and Sakura's genes in the baby could hold the key to some ancient power or prophecy. So they try to take the baby away from Naruto and Sakura to fulfill their own dark motives.
It could be Orochimaru. He might be interested in the baby's unique chakra, thinking he can use it for his experiments or to gain more power.
It could be a rogue ninja who has a vendetta against Naruto. Since Naruto is now married to Sakura, this antagonist might target Sakura as well to get to Naruto. Maybe this rogue ninja was once defeated by Naruto and now wants to take revenge by causing harm to his new family.
It could be a rogue ninja who has a vendetta against Naruto and wants to target his family. Maybe this ninja was once defeated by Naruto and now wants to take revenge by harming his loved ones, especially his and Sakura's child.
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.
Maybe the main antagonist is an evil organization that has been secretly infiltrating the village. They target Sakura because of her skills and knowledge. They deceive her into believing that her village is the real enemy, causing her to betray her comrades.
It could be Orochimaru. He has always been interested in Sasuke and might kidnap Sakura to use her as bait to get Sasuke back under his control. He could be after Sasuke's power and think that by using Sakura, he can manipulate Sasuke easily.
Well, perhaps in the fanfic, their baby has some special ninja abilities from birth. Naruto and Sakura are both proud and a bit worried. They seek advice from their old friends like Kakashi. They train the baby in a new way that combines Naruto's Rasengan - like techniques and Sakura's brute strength. And they face challenges from enemies who want to use the baby's power for evil.
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.
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.
Another possibility is a power - hungry ninja within the village who wants to take advantage of Sakura's situation. They might try to manipulate her or use her as a pawn in their scheme to gain more power. Since she's been abandoned, she may be more desperate and easier to influence, making her a prime target for this type of antagonist.
Itachi himself could be seen as the main antagonist in this scenario. After all, he is the one doing the kidnapping.