Maybe it's Kabuto. He could be searching for Sakura to use her as a bargaining chip against Naruto or Tsunade. Sakura hides under the desk when she senses his approach, and the 'pop' is Kabuto's jutsu misfiring near her hiding place.
Another possibility is a new, unknown ninja. This ninja has a vendetta against Konoha and targets Sakura. She takes refuge under the desk when she realizes she's being hunted. The 'pop' could be the ninja's unique attack method that startles Sakura while she's under the desk.
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.
Well, it could be about Sakura hiding under a desk during a pop - up dangerous situation in the Naruto world. Maybe she's using her medical skills secretly to help an injured comrade while under the desk.
One possible plot could be that Naruto and Sakura are hiding under a desk during a dangerous situation in the ninja village. Maybe they are on a mission and things go wrong, and they have to take cover under the desk while they plan their next move.
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.
Their relationship could develop in a more intimate way. Being in such a confined space like under the desk forces them to be closer physically. This might lead to them being more aware of each other's presence and start to see each other in a different light. For example, Naruto might notice Sakura's little nervous habits and find them endearing.
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.
In this fanfiction, the main antagonist could be a strict teacher. Sakura, being a boy with a free - spirited nature, often clashes with the teacher's rigid rules. The teacher always seems to be out to get Sakura, giving him unfair punishments and trying to suppress his creativity or individuality.
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.
It could be someone who doesn't want Sakura to become stronger. Maybe a rogue ninja who fears that a more powerful Sakura would be a threat to his plans. This antagonist might try to disrupt Naruto's training of Sakura by setting up various traps or distractions.
It could be a powerful dark wizard who wants to use Sakura's powers for his own evil purposes. He might be constantly trying to capture her or manipulate her into doing his bidding.