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.
Another reason could be that he senses danger. In the Naruto universe, there are many threats. As a baby, Naruto might not fully understand these threats but can sense the malevolent auras. His crying could be a natural reaction to this unease that he feels, like a warning sign that something bad might be about to happen.
Love. Just like any other character, Draco can be heartbroken in fanfiction. If he loses someone he loves, whether it's a friend or a romantic partner, he could cry. It shows his vulnerability and that he's not just the tough - guy Slytherin he often tries to be.
One possible reason could be that she's lost in an unfamiliar place. In the Naruto universe, it's a dangerous world for a baby. Maybe she got separated from her parents during an attack on the village. Another reason might be that she's hungry or not feeling well. Just like any baby, she could be crying because she needs something basic like food or warmth.
Isolation. Snape is a lonely character. He doesn't have many friends, and he is constantly in a difficult position between the Death Eaters and the Order of the Phoenix. His feeling of being alone and not being fully understood by anyone can lead to crying in fanfiction.
She might be crying out of frustration. For example, if she's been trying really hard to achieve a certain goal in the fanfiction, like mastering a new jutsu in a Naruto - themed fanfiction, but keeps failing. The stress and disappointment could lead to tears.
Another reason might be that he feels a great sense of guilt. For example, if he made a big mistake that had serious consequences for others, he would be overcome with guilt, which could manifest as 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.
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.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
One possible reason could be that she loses a Pokemon battle that she really thought she could win. In the Pokemon world, battles are very important to trainers, and losing one that she had high hopes for might make her cry.
Sakura might cry over Sasuke because of the distance between them. In many fanfictions, Sasuke goes off on his own journey, leaving Sakura behind. She misses him and the pain of separation makes her cry. Additionally, if Sasuke gets injured severely in a fight, Sakura, being a medic, might cry out of worry for his well - being and the possibility of losing him.