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.
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 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 family member who has a personal vendetta against Naruto and is the main instigator of his being shunned. Maybe an older cousin who is jealous of Naruto's potential.
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.
Maybe the main antagonist is a member of Naruto's own family who is power - hungry. This family member sees Naruto's growth to the Jounin level as a threat to their own position within the family. So, they manipulate the rest of the family into forgetting Naruto and excluding him from the family unit. They would stop at nothing to keep Naruto away and maintain their own power and influence.
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.
There could be a group of mean - spirited fairies. They see Sakura as an intruder in their territory, which might be a beautiful garden that Sakura often visits. To drive her away, they use their fairy magic to turn her into a cat, thinking that she will be less of a threat in that form. And they keep thwarting her attempts to turn back into a human throughout the fanfic.
Perhaps a new, powerful and mysterious ninja who has a vendetta against the Hidden Leaf Village where Sakura is from. He sees Zetsu as an accomplice of the village and targets both of them, causing chaos and danger in their lives. This new character could bring in a fresh and unexpected element of danger to the fanfic.
Perhaps an old enemy of Naruto or Sakura who was thought to be defeated but actually survived. They see the child as an easy target to get back at their parents. For example, if there was a rogue ninja from their past who held a grudge, they could come back and try to use the child to draw Naruto and Sakura into a trap. This antagonist would be very cunning and know all the weaknesses of Naruto and Sakura, which they could try to exploit through the child.