One possibility could be a story where Pokemon trainers enter the Vrains world of Yu - Gi - Oh. They might have to adapt their Pokemon battling skills to the digital dueling format. For example, Pikachu's electric attacks could be translated into some kind of digital energy in the Vrains world.
Another plot could involve a misunderstanding between Playmaker and Blue Angel that leads to a friendly duel to clear the air. During the duel, they learn more about each other's strategies and pasts, deepening their respect for one another. For example, Blue Angel could misunderstand Playmaker's motives in a certain situation and challenges him, but as the duel progresses, they realize they were both misinformed.
Their relationship could develop uniquely through a shared mission to protect a new and vulnerable part of the Vrains world. This common goal would force them to rely on each other more than ever, leading to a deeper bond. For instance, if a new area in Vrains was discovered that was full of weak but important programs, they could work together to fend off those who want to exploit it.
First, think about the characters. Combine the unique traits of Pokemon trainers and Yu - Gi - Oh duelists. For instance, Ash's determination in Pokemon and Yusaku's hacking skills in Yu - Gi - Oh Vrains. Then, create a conflict that involves both worlds, like a villain who wants to use Pokemon and Yu - Gi - Oh cards for evil. This will draw in fans from both franchises.
One great Pokemon Yugioh fanfic is 'The Dueling Trainers'. It combines the unique elements of both worlds. The story has trainers from the Pokemon universe suddenly finding themselves in a Yugioh - like card battle scenario. They have to use their Pokemon knowledge and skills to adapt to the new rules of the card game. It's really exciting as it shows how the different mechanics can interact in unexpected ways.
One idea could be a world where the Millennium Items from Yu - Gi - Oh have an effect on Pokemon. For example, the Millennium Puzzle might unlock a hidden power in a Pikachu. Another could be a story where the trainers in the Pokemon world start using Duel Disks from Yu - Gi - Oh to battle in a new, combined form of Pokemon and card battles. Maybe a powerful villain uses the dark powers of the Shadow Realm in Yu - Gi - Oh to control Pokemon for evil purposes.
Yugi and Ash could be an interesting pairing. Yugi's strategic mind from Yu - Gi - Oh duels could help Ash in his Pokemon battles. And Ash could introduce Yugi to the world of Pokemon training. Another pairing could be Kaiba and Gary. They both have that competitive streak. Kaiba might be intrigued by Gary's skills as a Pokemon trainer and Gary could be interested in Kaiba's high - tech Duel Disk.
One idea could be that a character from Naruto, like Naruto himself, gets transported into the world of Yu - Gi - Oh! VRAINS. He could learn about the Duel Monsters and Link VRAINS technology. Maybe he would start dueling using his ninja skills in a unique way, for example, using his shadow clone jutsu to create multiple copies of himself during a duel to confuse his opponent.
DeviantArt can also be a place to find Pokemon Yugioh fanfic. While it's mainly known for art, there are also some written works. You might have to do a bit more searching compared to the dedicated fanfic sites, but it can be worth it. Some artists also write fanfic based on their own art, which can give a unique perspective on the Pokemon Yugioh crossover.
Dialogue is important too. Make the characters talk in a way that's true to their original personalities. If Naruto is in Yu - Gi - Oh! VRAINS, he should still be enthusiastic and a bit of a goofball, but also show his growth as he faces new challenges. And when writing duels or battles, describe them vividly. Whether it's a ninja battle or a duel, the reader should be able to picture it clearly in their mind. Use lots of action verbs and sensory details to bring the scenes to life.