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.
It could also be related to his relationships. For example, if he had a fight with a close friend like Sasuke. Naruto values his friendships deeply, and any rift in those relationships can cause him great emotional distress. Jiraiya would then witness Naruto in this vulnerable state because of the pain of a broken or strained friendship.
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.'
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.
Maybe Harry is crying because he misses his parents. He often feels the pain of their absence deeply, and in this fanfic, when Sirius sees him, that could be the cause.
One possible reason could be that Naruto is feeling lonely. Despite having friends, there are times when his past as an orphan and the years of being shunned by the villagers resurfaces, making him feel isolated. Kakashi finding him in such a state might then lead to a heart - to - heart conversation about Naruto's inner struggles.
One reason could be the loss of a fellow shinobi. In the Naruto universe, comradeship is highly valued, and if Kotetsu were to lose someone close to him in battle or otherwise, it would be a very emotional moment that could lead to crying.
One possible reason could be the loss of a dear friend. Naruto forms deep bonds with his comrades, and if something were to happen to them, like Sasuke leaving again, it would break his heart and make him cry.
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.
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.
It could be the result of Naruto's own inner demons. Maybe he discovers some dark secret about his past, like his parents being involved in something he can't accept. This self - realization could be so traumatic that it makes him cry blood as he struggles to come to terms with it.
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.