It could also be related to his past traumas resurfacing. He has had a difficult childhood, being an outcast. Sometimes, certain events might trigger those old painful memories and cause him to break down in tears.
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.
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 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 be that Sakura betrays Naruto's trust. For example, if Naruto entrusts Sakura with a very important secret, like something related to his family or his new power he's developing, and Sakura reveals it to their enemies or uses it against Naruto in some way, that would be a huge blow to Naruto and could lead to him crying.
One reason could be extreme emotional pain. Maybe he witnesses the death of a very close friend or loved one in the fanfiction world. This overwhelming grief could cause such a physical manifestation as crying blood.
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.
Maybe Naruto discovers some dark secret about Tsunade's past that she has been trying to hide. For example, something related to her lost loved ones. Naruto, in his usual straightforward way, confronts Tsunade about it without realizing how much it would hurt her, and thus makes her cry.
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 reason could be the loss of his friends. Naruto values his friends deeply, and if he were to lose someone like Sasuke again, it would be devastating. Another reason might be the pressure of being the Hokage. The responsibilities are huge, and he might feel like he's not living up to the expectations of the village. Also, memories of his lonely childhood could resurface, making him feel sad and alone, leading to him crying himself to sleep.
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.
In fanfiction, Naruto might be crying because he has reached a breaking point in his journey. He has faced so many challenges, and Minato's appearance and his embrace make Naruto realize how much he has missed having a father. It could also be that Naruto is crying out of sheer happiness to finally be in his father's arms, even if it's in a somewhat surreal or spiritual way.