Perhaps he feels a sense of loneliness. Even though he has the Lost Boys, there might be times when he realizes that he is different from them. He is the only one who truly doesn't age, and this realization could hit him hard and cause him to cry, as shown in some fanfictions.
One reason could be to add a new level of conflict. If Hook is Peter's father, their battles in Neverland take on a whole new meaning. Another reason might be to explore a different origin story for Peter. Maybe the author wants to show that Peter got his adventurous spirit from Hook in some strange way.
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.
Maybe she sacrifices herself to save Peter Pan from a great danger, like a powerful enemy in Neverland.
One reason is that Peter Pan is a children's story, and such a dark and disturbing theme as abuse doesn't belong in it. It can be very harmful to the image of the original story and the characters that children love.
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.
It often makes the story more somber. When Peter Pan, who is usually seen as a carefree and happy character, cries, it changes the whole dynamic. It can bring out a sense of vulnerability that was not there before.
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.
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.