Perhaps Orochimaru. He might see Sakura's distraction from missing her chance as an opportunity to target Naruto or gain some advantage in his evil plans. He could manipulate the situation, making it even more difficult for Sakura to fix what she has missed.
The main antagonist could be a new character created specifically for this fanfiction. This character might be jealous of Sakura's relationship with Naruto and deliberately create situations that make Sakura miss her chances, all in an attempt to have Naruto for themselves.
In this fanfiction, perhaps Sakura misses the chance to confess her true feelings to Naruto. Maybe she hesitates for too long, and by the time she decides to act, Naruto has already moved on with someone else, like Hinata.
Sakura herself is obviously a main character. There could also be Naruto and Sasuke. Maybe Sakura misses her chance with Sasuke because she didn't speak up when she had the opportunity. Naruto might be involved as a friend who tries to encourage her but fails. Another character could be Kakashi, her sensei, who might have given her advice that she didn't follow, leading to her missing the chance.
Well, it could be about Sakura having a once - in - a - lifetime opportunity, like a chance to be with someone she loves or to achieve a great dream. But due to her hesitation or some unforeseen circumstances, she misses it. Maybe she was too shy to confess her feelings and the person she liked moved away. Or she didn't take a risk when a great opportunity for her ninja career presented itself and now she regrets it.
Obviously, the main character is Sakura.
Well, it could be about Sakura having a chance at something like a great opportunity in her career or a relationship with someone she really likes. But for some reason, she fails to take it. Maybe she was too scared or misjudged the situation.
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.
It could be a rogue ninja who has a grudge against Sakura. This ninja might set her up in a way that makes her lose her license.
It could be Orochimaru. He might be after some valuable information that Sakura has and she has to hide under the desk to avoid him. The 'pop' could be one of his experimental creatures suddenly showing up.
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.