One possible plot could be that Pikachu, as a girl, goes on an adventure to find a special type of berry that is said to have magical powers. Along the way, she meets other Pokémon who initially don't accept her because she's different. But through her kindness and determination, she wins them over and they all help her find the berry in the end.
Another way is to explore her relationships. If she's a girl, she might have a different dynamic with Ash (assuming it's set in the Pokémon anime universe). Maybe she's more of a confidante to Ash, listening to his problems and offering her own cute, Pokémon - perspective advice. Also, she could interact differently with male Pokémon, perhaps showing a bit of shyness or coyness at times.
It could change the way Pokémon interact with each other. For example, male Pokémon might show more chivalrous behavior towards a girl Pikachu. Also, it might inspire other fanfiction writers to create more stories with gender - bent Pokémon, leading to a more diverse range of stories in the Pokémon fanfiction community.
One possible plot could be that Pikachu, after being exposed to a strange form of energy in the Pokémon world, transforms into a girl. She then has to deal with the confusion of her new form while still having her Pikachu memories. She might struggle to fit into the Pokémon society in this new body, but also discovers new abilities or a deeper connection to certain types of Pokémon that she didn't have before.
One possibility could be that Pikachu, as a girl, goes on adventures with her trainer in a more nurturing way. For example, she might be more focused on taking care of smaller Pokémon they encounter during their journey. She could also use her electric powers in a more delicate and strategic manner, like using small electric jolts to communicate with other Pokémon rather than just for battle.
The change in its appearance can make it scary. For example, if its usually cute yellow fur turns dark or if its bright red cheeks become a sinister red glow. Also, if it starts to behave in an uncharacteristic way, like making menacing noises instead of its usual cute sounds.
Obviously, the main characters are usually Pikachu. But sometimes, there could be other Pokémon that play important supporting roles. For instance, a Pichu could be a sidekick or a younger Pokémon that the Pikachus are protecting.
One interesting plot could be two Pikachus from different regions meeting and learning about each other's unique electric attacks. For example, one Pikachu might know a special move that the other has never seen before. They could then teach each other and become stronger together.
Naruto would probably be really excited. He'd treat Pikachu like a new friend and teammate. He might try to learn all about Pikachu's powers and how it can help in battles. For example, he'd be eager to see Pikachu use Thunderbolt in a fight against an enemy ninja.