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 the main antagonist is a dark spirit that haunts the place where Kakashi's mother is. This spirit doesn't want Kakashi to reunite with his mother because it feeds on the negative emotions of separation. So it tries to create all sorts of obstacles like illusions and traps to keep Kakashi away.
The main antagonist might be a dark sorcerer. This sorcerer has put a spell on Spyro's mother long ago, trapping her. He doesn't want Spyro to find her because he fears that together they will be strong enough to break his power. He uses his minions to try and stop Spyro during his journey to find his mother.
One possible plot could be that Kakashi, while on a mission in a mysterious forest, stumbles upon a strange and powerful force. As he investigates, he is suddenly transported to a different realm where he meets his mother. His mother reveals secrets about his family's past and the origin of his Sharingan. Then they have an emotional conversation about how much she missed seeing him grow up.
It could be Frieza. Since Frieza has a history of hating the Saiyans, he might see Goku's sister as a new threat and try to eliminate her.
Maybe a dark version of Neji himself could be the antagonist. This could be a Neji from a parallel world where he succumbed to hatred and envy. He might try to destroy the 'good' Neji and take over his life, believing that his way is the right way and that the other Neji is a weak version.
Perhaps there is no traditional antagonist. Instead, the conflict could be within Percy himself. His future self might have some dark secrets or regrets that Percy in the present doesn't want to face. So, in a sense, Percy's own denial or fear could be the 'antagonist' in this fanfiction.
It could be a dark wizard who is trying to prevent Teddy from meeting his father. This wizard might be afraid that Teddy will gain some powerful knowledge or magic from his father that could be used against him.
Perhaps Neji's own insecurities could be the main antagonist in a sense. When he meets his alternate self, he might start to feel inadequate or question his own identity. This internal struggle could be the main obstacle they have to overcome rather than an external enemy.
It could be someone who doesn't want Naruto and his sister to unite. Maybe a rogue ninja who fears their combined power. He might try to drive a wedge between them by spreading false rumors or causing misunderstandings.
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.