It could be a Pokemon itself. Maybe a dark - type Pokemon with a grudge against humans and Pikachu in particular. This Pokemon could be using its powers to cause chaos in the city, and Pikachu has to figure out its motives and stop it before it's too late.
A more complex plot could involve Detective Pikachu trying to figure out a conspiracy among a group of humans who are trying to use Pokemon for illegal and unethical experiments. This would involve Pikachu teaming up with other Pokemon and human allies, like Tim, to expose the bad guys. They would have to face many obstacles and dangerous Pokemon controlled by the villains along the way.
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.
In fanfiction, Pikachu's Mega Evolution often brings out new and exciting abilities. Writers might imagine Pikachu growing larger, with enhanced electric powers. It could have the ability to create more powerful thunderbolts or even manipulate electricity in new ways, like forming shields or sending out electric waves to paralyze opponents from a greater distance.
They could be in a fanfiction where they are forced to work together against a common enemy like a powerful trainer who wants to capture them both. Pikachu's speed and strong electric attacks combined with Pachirisu's cute charm and quick thinking can make for an interesting dynamic.
One great fanfiction idea could be a story where Pachirisu and Pikachu team up to save their forest home from a mysterious dark force. They use their unique electric powers in combination to fend off the threat and in the process, learn more about each other's strengths and weaknesses.
In some Pokemon fanfiction, Pikachu's ageing might be shown through physical changes like a slightly greying of its fur. This could symbolize the passage of time and the experiences it has had. For example, an older Pikachu might be a bit slower in battles but wiser in its strategies, having learned from countless encounters over the years.
One common reason could be jealousy among other Pokemon. Some Pokemon might be jealous of Pikachu's closeness to Ash and its popularity. So, they might plot against it and end up killing it. Another reason could be a misunderstanding. For instance, a wild Pokemon might misinterpret Pikachu's actions as a threat and attack it fatally.
There's 'The Great Pikachu WC Debut'. This fanfic focuses on Pikachu's first time in the Wonder Contest. It's really detailed in terms of how Pikachu prepares for the contest, from choosing the right moves to getting into the right mindset. It also has some interesting interactions with other Pokemon trainers at the contest venue.
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.