There could also be elements within the ninja villages themselves that oppose Naruto and Jiraiya leaving. These could be power - hungry individuals who fear that Naruto will gain too much influence outside the village and come back stronger, threatening their own positions of power. So they send their own agents to stop Naruto and Jiraiya from leaving or to disrupt their journey.
Some fanfictions might feature rogue ninja as antagonists. These rogue ninja are after the bounty on Naruto's head or they are trying to steal Jiraiya's knowledge. They attack Naruto and Jiraiya during their travels, making it difficult for them to reach their destination.
Pain is often one of the main antagonists. Since in the original story, Pain was the one who ultimately killed Jiraiya. So in fanfictions where Naruto saves Jiraiya, Pain is a natural choice to be the bad guy. Another common antagonist could be Orochimaru. He had his own vendetta against Jiraiya and the Hidden Leaf Village. He might be trying to use Jiraiya for some evil experiment or to gain access to the secrets of the Sage Mode.
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.
It could be a group of rogue ninjas from the new time period who see Jiraiya as a threat to their plans. Since he has different skills and knowledge, they might want to eliminate him.
Maybe they leave to find a cure for a strange disease that has started to affect the ninja world. Jiraiya has some clues about a special herb in a far - off region and they embark on a journey. During this, Naruto learns about the importance of perseverance from Jiraiya. They face many enemies who don't want them to succeed in their mission.
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.
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.
There could also be other characters from the Naruto universe that play important roles. For instance, Tsunade might be involved as she has a connection to Jiraiya. She could offer additional guidance or be a source of conflict when she disagrees with Jiraiya's training methods for Naruto.
Well, obviously Naruto and Jiraiya are the main characters. Naruto is the young ninja with the Nine - Tails sealed inside him, eager to learn and grow stronger. Jiraiya is the pervy but highly skilled and wise ninja who takes Naruto under his wing as an apprentice.
Well, the main antagonists could be a group of rogue ninja who are hired by a powerful nation to take down Naruto. Since he is unkillable, they would have to use more underhanded tactics like trying to isolate him from his friends and allies. Or perhaps there is a dark force that is awakened by Naruto's unkillable state, thinking that he is a threat to the balance of the ninja world. This dark force could then become the main antagonist, trying to destroy Naruto at all costs.
Obviously, Naruto and Jiraiya would be the main characters. Naruto, the protagonist of the original series, and Jiraiya, his mentor. They have a deep connection, and any fanfiction about them meeting would revolve around their relationship.