Maybe a rogue ninja from their own village who has a grudge against Kakashi or Rin. This ninja could be jealous of their relationship and the new life they are about to bring into the world. He or she might try to spread false rumors about them first to isolate them, and then launch a direct attack.
The Akatsuki could also be antagonists. They might view the baby as a potential threat in the future, especially if they believe it could grow up to be a powerful ninja. So they send some of their members to disrupt Rin's pregnancy, like Deidara, who could use his explosive jutsu to create chaos around them.
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.
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 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 a rogue ninja from a hidden village who has a vendetta against Naruto for some reason. Maybe Naruto unknowingly disrupted this ninja's plans in the past, and now the ninja wants revenge. This would set up a situation where Naruto is in danger and needs Rin's help to be rescued.
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.
Maybe it could be a new forensic scientist who is jealous of Brennan's position and sees her pregnancy as a weakness to exploit.
The main antagonist could be LeFou. He might be jealous of Gaston's new relationship with Belle and the fact that they are having a baby. So, he could try to create problems between them, like spreading false rumors in the village about Belle's past or Gaston's intentions.
There could be an internal antagonist within Konoha as well. Maybe a jealous ninja who has always had a crush on Shikamaru or envied Ino's skills. This person could spread false rumors about Ino's pregnancy, causing unnecessary stress and drama for the couple. They might try to drive a wedge between Shikamaru and Ino during this vulnerable time.
It could be Nancy's over - controlling mother. She might be against the pregnancy and try to force Nancy to make certain decisions, like giving the baby up for adoption against her will.
It could be one of their ex - partners who is jealous of their new relationship and the upcoming baby. This person might try to create misunderstandings between Toby and Spencer.