One possible plot could be that the Pokemon trainers discover a hidden hot spring in a secluded area of the Pokemon world. While they are enjoying the hot spring, some rare and shy Pokemon are attracted to the warmth and come out. The trainers then have to decide whether to try and catch these Pokemon or just let them be and enjoy this unique moment of co - existence.
A plot might involve a group of Pokemon getting sick. A wise old Pokemon leads them to a magical hot spring that has healing properties. As the Pokemon soak in the spring, they start to feel better. Meanwhile, the trainers are worried and search for their Pokemon. When they find them at the hot spring, they learn about the special place and vow to protect it. This could also lead to new friendships between different types of Pokemon.
In a Pokemon hot spring fanfiction, the plot could be that there is a competition among trainers to reach a famous hot spring first. The hot spring is said to make Pokemon evolve faster. Along the way, they face various challenges like difficult terrains and other trainers who want to stop them. When they finally reach the hot spring, they find out that it's not about making Pokemon evolve faster but about strengthening the bond between the trainer and the Pokemon.
The main characters would likely be the Pokemon trainers. Ash, Misty, and Brock from the original series are obvious choices as they are well - known and loved. They could be traveling and stumble upon a hot spring area. Their Pokemon, like Pikachu, Togepi, and Onix, would also be part of the story, enjoying the hot spring or having adventures around it.
One interesting plot could be that Ben, using his Omnitrix, accidentally lands in the Pokemon world. He teams up with Ash and Pikachu to stop an evil organization that is trying to use both Pokemon and alien technology. For example, they might be creating hybrid creatures using Pokemon DNA and alien powers. Ben's different alien forms could have unique interactions with the Pokemon. His Four Arms form could be really strong in Pokemon battles, while his XLR8 form could be used to quickly traverse the Pokemon world to reach different areas in time to stop the villains.
One possible plot could be that Ash is transformed into a rare and powerful Pokemon like Mewtwo. He then has to navigate the Pokemon world from a different perspective. He discovers new abilities and strengths he didn't know about before. And he uses his knowledge of being a trainer to communicate with other Pokemon and form alliances to face the challenges that come his way.
Maybe Ursula is a Pokemon researcher in this fanfiction. Naruto, with his curious nature, decides to help her in her research. Along the way, they discover a new type of Pokemon that has special powers. Their adventure to understand and protect this new Pokemon could form the basis of the story. It would involve Naruto using his combat skills and Ursula her knowledge of Pokemon.
One possible plot could be that the Pokemon and Justice League members have to team up to stop an evil force that is trying to take over both the Pokemon world and the cities protected by the Justice League. Maybe a powerful, shadowy villain has discovered a way to use Pokemon powers in the human world in a very destructive way, and only by combining the unique abilities of the Pokemon and the superpowers of the Justice League can they hope to defeat this new threat.
One possible plot could be Ash being chosen by Arceus to save the world from a new, mysterious threat that even the Legendary Pokemon are powerless against. He has to travel to different regions and form bonds with various Legendary Pokemon along the way, using their combined powers to face the danger.
One possible plot could be that Pokemon are used in the battlefields of Call of Duty. For example, trainers send out their Pokemon to scout the area, detect hidden enemies or even engage in combat. Pikachu could use its electric attacks to take out groups of enemy soldiers hiding behind cover, while Charizard could provide air support by breathing fire on enemy positions from above.
One possible interesting plot could be that the RWBY characters are transported into the Pokemon world and have to learn how to catch and train Pokemon in order to find a way back home. They might struggle with the different battle styles compared to their usual combat in Remnant.
One possible plot could be a trainer in the Pokemon world discovers a strange worm - like Pokemon that has abilities never seen before. This Pokemon could be a key to unlocking a hidden power within the region that an evil team is also after. The trainer has to protect the worm - like Pokemon and use its unique powers to defeat the bad guys.
One possible plot could be that Mario and Luigi are exploring a new world and accidentally stumble upon the Pokemon world. They team up with Ash and Pikachu to stop Bowser who has teamed up with Team Rocket to steal all the Pokeballs and use the Pokemon's power to take over both the Mushroom Kingdom and the Pokemon world.