They might cry because of the threat to their home in Neverland. Maybe Captain Hook is up to some new mischief that endangers the fairy glades.
It could be due to a rift between them and Peter Pan. For example, if Peter makes a decision that affects the fairies without consulting them, like bringing new people into Neverland who disrupt the delicate balance of the magical world.
At night, the fairies' cries can have different effects. Their cries might attract unwanted attention, like from the pirates. Since the pirates are more active at night in Neverland, they could hear the fairies' cries and try to capture them for their own purposes, such as using their magic. So the night puts the crying fairies in more danger.
One popular theme is the exploration of eternal youth. Since Peter Pan doesn't grow up, fanfiction often delves into what that really means. Another theme could be the relationship between belief and magic. If the characters believe in fairies, it often leads to magical things happening. Also, the idea of friendship in Neverland is a big theme. Peter's friendships with the Lost Boys and his relationship with Wendy are often explored more deeply in fanfiction.
Perhaps it's a story where the fairies cry because they sense some dark force approaching Neverland. They might be worried about the safety of Peter Pan and the Lost Boys. In the fanfiction, Peter could be initially oblivious to this danger but then realizes it when he sees the fairies' distress and decides to fight against this new threat.
Maybe they cried because they sensed some approaching danger in the night. In many Peter Pan fanfictions, fairies are very sensitive to the changes in Neverland. If there were some dark forces or threats emerging, like Captain Hook planning a new evil scheme, their delicate nature would make them cry out of fear or worry.
It could be about the fairies crying because Peter Pan has forgotten them. Maybe he's been too caught up with Wendy and the Lost Boys and has neglected his relationship with the fairies.
The main characters could be a young girl who has just arrived in Neverland. She could be the cause of the fairies crying, either because she doesn't understand their ways and accidentally offends them, or because she has a special power that scares them. Peter Pan then has to deal with this new situation, trying to protect the girl from the fairies' wrath while also making peace between them.
Wendy could also be the main character. She might have a special connection with the fairies that no one else knows about. So when the fairies cry, she steps in to help, using her own unique understanding of Neverland.
Peter Pan himself is very intriguing. His carefree nature and refusal to grow up offer a lot to write about. Wendy is also interesting. She comes from the 'real' world but gets drawn into the magic of Neverland. And Captain Hook, with his villainous ways and his obsession with Peter Pan, makes for a great character to write about in fanfiction.
Well, in the original Peter Pan story, there are hints of a special relationship between them. Fanfiction writers are drawn to this. Tinkerbell's jealousy when Peter shows interest in Wendy, for example, shows that there could be more to their relationship. Also, the fact that they live in the magical world of Neverland gives a lot of scope for creative and romantic storylines about their love.
One reason could be that Tony is trying to protect Peter. He might think that by being harsh and making Peter cry, he can keep Peter away from a dangerous situation. For instance, if there's a really tough mission coming up, Tony might push Peter away by being cruel so that Peter doesn't get involved.