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.
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.
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.
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.
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.
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.
In this fanfiction scenario, the emotional depth would be significant. Naruto crying while Jiraiya covers him could signify a moment of breakdown for Naruto. It could be that he has failed at something important, like a mission, and Jiraiya's covering is his way of saying it's okay. It could also be related to Naruto's past traumas resurfacing. Jiraiya, being the experienced and caring mentor, offers his protection both physically and emotionally. This simple act can hold a lot of unspoken emotions between them, such as trust, love, and the hope that Jiraiya can make things better for Naruto.
Maybe Kurenai is doubting her abilities as a ninja and a teacher. Naruto then shows her all the ways she has influenced the lives of the young ninjas in Konoha. He gives her examples of how her students look up to her and how she has taught them valuable skills. Naruto's belief in her could boost her confidence.
Perhaps Naruto has just lost a fight against a powerful enemy and is feeling defeated. His crying is a result of his frustration and self - doubt. Jiraiya, covering him, then begins to train Naruto more intensively to help him overcome his weaknesses. Or it could be that Naruto has witnessed something truly horrifying in the ninja world, like a massacre. Jiraiya's act of covering him is the start of him guiding Naruto to understand the darker aspects of their world and how to face them bravely.
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.
Maybe she had a bad memory from her past resurface. For example, something related to her time in Mossad or her family issues could have triggered her emotions.