One possible fanfiction could be that James loses his beloved Weezing in a battle. He has had Weezing since he was a child, and it was like his only true friend in Team Rocket. So when it faints and doesn't get up, he starts crying. He realizes how cruel the world of Pokemon battles can be and has a moment of self - reflection about his life in Team Rocket.
Suppose James enters a Pokemon beauty contest for his favorite Pokemon. But due to some underhanded tactics by other contestants, his Pokemon loses. James, who had put so much hope and effort into it, starts crying as he feels he let his Pokemon down.
It's possible that he's crying over a failed romance. He might have fallen in love with someone who didn't feel the same way, or something tragic happened in their relationship. Love can be a very powerful and painful emotion, even for a young wizard like James Sirius Potter.
I remember a fanfic titled 'Hidden Fears'. In it, James Potter cries when he faces a situation where he feels he might lose Lily. It's a very emotional piece that explores his love for her and his insecurities. The author does a great job of building up the tension and then releasing it through James' tears.
One scenario could be that Wendy's Pokemon was stolen by a villain. This would be a very distressing situation for her as she would be worried about the safety and well - being of her Pokemon.
In some fanfictions, Alain's crying could be related to his past traumas or difficult relationships. Maybe he had a rough childhood that is explored in the story, and a particular event triggers his tears. To find these fanfictions, use specific search terms like 'Alain's emotional breakdown in Pokemon fanfiction' on search engines. Also, look for fan - created anthologies or collections that might feature such stories.
One popular Pokemon crying fanfic could be about a Pokemon that gets separated from its trainer and cries out of loneliness. For example, in a story where Pikachu is lost in a big forest and it cries as it tries to find its way back to Ash. It shows the emotional bond between the Pokemon and the trainer.
A simple emotional trigger could be homesickness. Whitney might be far away from her hometown in the Pokemon world. She misses her family, friends, and the familiar places. This loneliness and longing can lead to her crying.
It could also be that Whitney is separated from her Pokemon. For example, there could be some sort of Pokemon - stealing gang in the story. They manage to take her Pokemon away from her. She loves her Pokemon like family, and the thought of being without them makes her break down in tears.