A powerful and corrupted Gengar could be a great antagonist. Gengar could use its ghost - type powers to create illusions and traps within the mystery dungeon, making it difficult for Pikachu and its friends to progress. It might be after a powerful artifact hidden in the dungeon and will stop at nothing to get it.
Perhaps a Mega - evolved Absol. Absol is often associated with disasters, and in the fanfic, a Mega - Absol could believe that by causing chaos in the Mystery Dungeon, it can prevent a greater catastrophe. It sees Pikachu and the other Pokemon as obstacles in its plan and tries to defeat them at every turn.
A group of Team Rocket - like villains could be the main antagonists. They might want to capture Pikachu while it's in the process of evolving because they believe that an evolving Pikachu would have some special power that they could use for their evil plans. They constantly try to disrupt Pikachu's evolution and the bond between Pikachu and its trainer.
Team Rocket could still be the main antagonists. They might see Ash as a Pikachu and try to capture him more than ever, thinking he's a special Pikachu. Maybe they believe he has some sort of new power because of his transformation.
A powerful and greedy Team Rocket - like organization could be the main antagonist. They might be trying to take over the Mystery Dungeon world for their own gain, stealing resources and capturing Pokemon.
It could be a trainer who hates Pikachu and wants to capture all of them. This would put Ash, as a Pikachu fan, in direct conflict with this trainer.
Another possibility is a rival trainer who has a Pokemon that is weak against Raichu. This trainer might try to prevent Pikachu from evolving to keep their own Pokemon's advantage in battles. They could try to steal Pikachu's food or training resources to slow down its growth and evolution.
One idea could be that Pikachu wakes up in a strange part of the mystery dungeon with no memory of how it got there. It has to team up with other Pokemon it meets along the way, like a Charmander and a Squirtle, to figure out the mystery of the dungeon and also find a way to get back home.
Another common theme is self - discovery. Pikachu may start out not knowing its full potential, but through the experiences in the mystery dungeon, it learns more about itself. It might discover new abilities or learn more about its personality traits, like its courage or loyalty. This theme adds an interesting layer of character development to the fanfictions.
It could be a rogue Pokémon trainer who wants to capture Ash - now as Pikachu - for his own collection. This trainer might have a cruel streak and not care about the well - being of Pokémon.
One possible main character could be Pikachu. Since Pikachu is a very popular Pokemon, it would be interesting to see it in a prison setting in the Pokemon Mystery Dungeon. It could use its electric powers in unique ways to deal with the prison environment and other Pokemon.
An organization of rogue scientists who want to experiment on Pokemon could be the main antagonist. They might be trying to create super - powerful mutant Pokemon or find a way to control all Pokemon. If you're reborn as a Pokemon, they might capture you for their experiments. This could lead to a story where you have to escape from their labs and expose their evil plans to the rest of the Pokemon world.