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.
Jiraiya would probably offer some words of wisdom. He has a lot of life experience, so he might tell Naruto that crying is not a sign of weakness but a way to let out pent - up emotions. For example, he could say something like 'Boy, those tears are like the rain that nourishes the seeds of your growth.'
In fanfiction, Jiraiya seeing Naruto as Hokage can be a very emotional moment. It could be a vision Jiraiya has in a story where he's still alive, or perhaps it's a memory in a story set after his death. This often shows Jiraiya's pride in Naruto and his belief in Naruto's potential to lead the village.
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.
One common theme is the passing of the torch. Jiraiya, who was part of the older generation, sees Naruto taking on the leadership role, representing the new era. Another theme is the realization of dreams. Jiraiya always hoped for Naruto's success, and seeing him as Hokage is that dream coming true.
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.
Sakura may react with a sense of urgency. She would drop whatever she was doing and rush to Naruto's side. She'd be worried that something truly terrible has happened. If Naruto is hesitant to talk, Sakura might just sit quietly with him, waiting for him to open up. This would show her patience and understanding, and also how much she values Naruto as a friend.
The plot might involve Naruto crying due to a misunderstanding with his friends. Kakashi witnesses this and steps in to mediate. He first calms Naruto down and then arranges for Naruto and his friends to have an open conversation. During this process, Kakashi shares some wisdom about friendship and communication, helping them resolve their differences.
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.
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.