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.
It could be a powerful rogue ninja who has a vendetta against Kakashi and sees his daughter as a way to get revenge. This antagonist might try to use her as a bait to lure Kakashi or Naruto into a trap.
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 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.
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.
The mother's new partner. He doesn't want the forgotten daughter to be part of the family as he fears she will disrupt the new family dynamic he has been trying to build. He might use various means to keep her away from the family.
It could be a new group of rogue ninjas who oppose the ideals of the Hidden Leaf Village. They might target Kakashi's daughter because of her connection to Kakashi and Naruto, seeing her as a symbol of the village's new generation of strength.
Another option is a power - hungry wizard from within the Ministry of Magic. They might see Harry's daughter as a tool to gain more power. They could try to manipulate her or create situations where she is framed for things she didn't do, all in an attempt to control her and use her connection to Harry for their own political gain.
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.
It could be an original character created just for the fanfiction. Maybe a mysterious ninja woman who crossed paths with Kakashi during a mission and they had a brief but intense relationship.
A group of rogue demigods could be the main antagonists. They might be jealous of the attention the daughter gets because of her parents. So, they plot to make her life difficult and try to drive a wedge between her and the other demigods.