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.'
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.
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.
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.
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.
One possible reason could be that he is lonely. In many fanfictions, Naruto is often ostracized as a baby due to the Nine - Tails inside him. He might be crying because he feels the lack of a warm, loving presence around him.
Sakura could be the one to find him crying. She has known Naruto for a long time and they are comrades. If Naruto is in a vulnerable state, she might stumble upon him.
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.
She might immediately go to comfort him. Hinata has always cared deeply for Naruto, so seeing him cry would likely trigger her protective and empathetic side.