It could be Orochimaru. Since Orochimaru has a long - standing feud with Jiraiya and is always up to no good. If Naruto ditches Jiraiya, Orochimaru might see this as an opportunity to manipulate Naruto. He could try to convince Naruto that Jiraiya was holding him back and that he can offer Naruto more power, all while having his own evil plans for Naruto.
One possible plot could be that Naruto has a major disagreement with Jiraiya over his training methods. Maybe Naruto feels that Jiraiya is being too hard on him or not focusing on the right aspects of his growth. So, in a fit of anger or determination, he decides to ditch Jiraiya and go off on his own to train in a new way.
It could be Orochimaru. Since he has a history with Jiraiya, he might target Naruto while he's under Jiraiya's tutelage, seeing Naruto as a potential threat in the future. Orochimaru could try to steal Naruto's power or use him in some dark experiments.
Maybe the main antagonist could be an older version of Madara Uchiha who has somehow found a way to manipulate time as well. He might be trying to change the past in a way that benefits him and his grand plan for the ninja world, which would put him in direct conflict with Jiraiya.
It could be the person who spreads false rumors about Jiraiya to Naruto. This person might be an enemy of Jiraiya who wants to drive a wedge between him and Naruto. By making Naruto ignore Jiraiya, they hope to weaken both of them.
Perhaps an old enemy of Jiraiya who was thought to be defeated but has now resurfaced. This antagonist targets Boruto to get to Jiraiya, thinking that by harming Boruto, he can draw Jiraiya out and finally get his revenge. He would be a powerful and cunning foe, making it difficult for Jiraiya and Boruto to face him.
Perhaps in this fanfiction, Jiraiya discovers that Naruto is going to be the cause of a major catastrophe in the future. He might have seen a prophecy or some sort of sign that convinces him Naruto has to die to prevent this. It could also be that Jiraiya has been misled by false information about Naruto, which makes him think that Naruto has become an evil force that needs to be eliminated.
One possible reason could be that Naruto feels he has learned all he can from Jiraiya at that point. Maybe he has reached a level in his training where he believes he needs new experiences and challenges that Jiraiya can no longer provide.
Another reason could be that Jiraiya has some doubts about Naruto's readiness or potential. He might think that Naruto is not yet at the level where he can fully benefit from Jiraiya's training. For example, Naruto may lack some basic skills or knowledge that Jiraiya believes are necessary prerequisites for his more advanced training.
One possible reason could be that in this fanfiction, Jiraiya might be preoccupied with other important matters. Maybe he has a secret mission that demands his full attention and he simply doesn't have the time to train Naruto. Another reason could be that there is some sort of conflict or misunderstanding between them that prevents Jiraiya from taking Naruto under his wing. For example, Naruto might have unknowingly offended Jiraiya in some way, or there could be a prophecy or external force that is keeping them apart for the time being.
Obviously, Naruto and Jiraiya are the main characters. Naruto is the young and energetic ninja with big dreams, while Jiraiya is the experienced and somewhat pervy sage who has a lot to teach Naruto.