Jiraiya's comfort gives Naruto the confidence to face his fears. For example, if Naruto was crying because he was afraid of a powerful enemy, Jiraiya's words of wisdom and support would make him more determined to train harder and find a way to defeat that enemy in the future.
Jiraiya's comfort can also make Naruto more empathetic. If Naruto was crying because of a misunderstanding with a friend, Jiraiya's calming presence and advice would make Naruto realize the importance of communication. In the future, Naruto would be more likely to reach out to others first, resolve conflicts amicably, and build stronger relationships because of this experience of being comforted by Jiraiya.
Jiraiya might comfort Naruto by sharing his own experiences. He could tell Naruto about the times he faced difficulties and how he overcame them. For example, he might talk about his training with the toads and how he grew stronger through perseverance.
It could be that Naruto has lost a dear friend. He is overwhelmed with grief. Jiraiya comes to his side. He doesn't say much at first but just gives Naruto a big hug. Then he starts to talk about the impermanence of life and how those who are gone would want Naruto to keep moving forward and be strong for their sake.
The plot could be that Naruto is crying due to the pressure of being the Jinchuriki. Jiraiya comforts him by saying that his strength is not just in the Nine - Tails but in his own heart. He gives Naruto the fan as a reminder of their bond and that he'll always be there for him, even if not physically.
One common theme is mentorship. Jiraiya acts as a mentor to Naruto, guiding him not just in ninjutsu but also in life. Another theme is emotional healing. Naruto often has a lot of emotional baggage, and Jiraiya helps him work through it.
One possible reason could be that Naruto is feeling lonely. Despite having friends, he still has moments when the weight of his past, like being an orphan and ostracized in the village as a child, hits him hard. Jiraiya might see Naruto crying because of these memories resurfacing.
The training makes Naruto more confident in his abilities. Jiraiya constantly challenges Naruto and as Naruto overcomes these challenges, he realizes his own strength. He starts to believe in himself more, which is evident in the way he faces stronger opponents without hesitation later on. Also, Jiraiya's teachings about the ninja way and the importance of protecting those you love make Naruto more determined and focused on his goals.
Their relationship would be very strong. Jiraiya would see Naruto as not just a student, but also as a connection to Minato. He would be strict but also very affectionate. Naruto would look up to Jiraiya as a father figure, since he never really had one. They would share many adventures together, with Jiraiya teaching Naruto about life, love, and ninjutsu.
At first, Naruto might isolate himself. He doesn't want to be around others as he is so consumed by his grief. He just sits in his room or goes to a quiet place where he can cry alone and think about Jiraiya.
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 fanfiction could be that Naruto is crying after a particularly tough mission where he lost a comrade. Jiraiya finds him and offers his fan, which has a special significance. He tells Naruto about his own losses and how he overcame them, inspiring Naruto to keep going.