In a fanfiction, James could return to his old family home and find it in ruins. All the memories of his childhood come flooding back, and he realizes how much he has lost. He cries for the innocence of his youth and the family he once had, and this could be a moment of him deciding to change his ways and find a new purpose in life.
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.
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.
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.
Well, in some fanfictions, the plot could revolve around their family. They might decide to have a family of their own, and the story could focus on how they raise their children in the Pokemon world. This could include teaching their kids about Pokemon, dealing with the kids' Pokemon adventures, and also protecting their family from any threats that might come their way because of their past associations. It could also be about them traveling the world together as a married couple, exploring new regions and discovering new Pokemon species while strengthening their relationship along the way.
Maybe Wendy is crying because her favorite Pokemon got hurt in the fanfiction. It's really sad when a beloved Pokemon is in pain.
The plot might involve Naruto crying due to a misunderstanding with his friends. Kakashi witnesses this and steps in to mediate. He first calms Naruto down and then arranges for Naruto and his friends to have an open conversation. During this process, Kakashi shares some wisdom about friendship and communication, helping them resolve their differences.
The plot could revolve around how James and Sarah adjust to their new roles as expectant parents. They could start taking parenting classes together. Along the way, they might have some disagreements about things like the type of delivery they want or how to decorate the nursery. However, through communication and understanding, they work out their differences and grow closer as a couple. As the due date approaches, they are fully prepared and excited for the arrival of their baby.
His injury might be caused by a malfunction of one of Team Rocket's inventions. For example, a new type of Pokeball - capturing device could backfire and injure James. This would cause chaos within Team Rocket as they try to fix the device and also take care of their injured comrade. Meanwhile, other characters might take advantage of Team Rocket's momentary weakness.
One possible reason could be her separation from her Pokemon. In the Pokemon world, the bond between trainers and their Pokemon is extremely strong. If Lillie were to be separated from a beloved Pokemon, perhaps due to some unforeseen circumstances like it being captured by a villainous team, she would be heartbroken and cry. Another reason might be related to her family. Maybe there are secrets within her family that are revealed in the fanfiction, and these revelations are so overwhelming that she can't help but cry.
One possible storyline could be that Jessie and James, after years of being Team Rocket members, decide to leave that life behind. They realize their love for each other while on a Pokemon adventure. In the fanfiction, they might start a new life in a peaceful Pokemon - filled region, perhaps opening a Pokemon - themed cafe. Their Pokemon would also be part of their new life, with Meowth helping out in the cafe.
One possible reason could be that Pikachu is separated from Ash. In many fanfictions, their bond is so strong that being apart would be extremely distressing for Pikachu, leading it to cry.