One possible scenario in fanfiction could be that Bonnie catches a strange illness from a new Pokemon she encounters in the Kalos region. This illness might cause her to lose her energy and enthusiasm, which are her usual traits. Her friends, Clemont and the protagonist, would then search for a cure.
Well, she might become more vulnerable. Usually, Bonnie is full of life and always ready for an adventure. But when sick, she could be more dependent on others like Clemont. Her positive attitude might also be affected, and she could start to worry about not being able to keep up with her friends.
I'm not sure of a specific one off - hand. But you could try searching on fanfiction - dedicated websites like FanFiction.net or Archive of Our Own. Just type in 'Pokemon X and Y Bonnie hurt' in their search bars, and you should be able to find some relevant stories.
One possible fanfiction could be where Bonnie catches a rare Pokemon - related illness. Maybe she got it from exploring an old, mysterious forest in the Pokemon XY world. Her friends, like Ash and Clemont, would then have to search for a cure. They might visit different Pokemon Centers and ask the Nurse Joys for help, but find that this illness is something they've never seen before.
One possible fanfiction could be about Bonnie getting hurt during a Pokemon battle. Maybe she tries to protect her Pokemon and ends up getting injured herself. It could show her courage and the bond between her and her Pokemon.
It could be that Bonnie's sickness is a psychological one. Maybe she witnessed something really traumatic during a Pokemon encounter, like a powerful and cruel Pokemon attacking a weaker one. This shock made her fall ill. Ash and Clemont would try to help her overcome this trauma by taking her to peaceful places and showing her the good in the Pokemon world, hoping it will heal her mind and body.
One idea could be a story where Naruto is transported to the Pokemon X and Y world. He could use his ninja skills to catch Pokemon in unique ways. For example, he might use his shadow clone jutsu to surround a wild Pokemon and then throw a Poke Ball with perfect accuracy.
A plot where Shauna participates in a high - stakes Pokemon tournament. She faces off against tough opponents, and each battle teaches her something new about herself and her Pokemon. The fanfiction could focus on her mental and emotional journey during the tournament, from the nerves before the first battle to the elation of victory or the disappointment of defeat.
It could be about Shauna's journey in the Kalos region. Maybe it focuses on her interactions with the player character, her growth as a trainer, and her experiences with different Pokemon. For example, it might detail how she overcomes challenges in battles and forms deeper bonds with her Pokemon.
One great fanfiction is 'A Journey with Serena and Calem'. It focuses on their adventures in the Kalos region, exploring how their relationship develops during battles and while facing various challenges. The author does a wonderful job of capturing their personalities as seen in the game.