Well, for a Power puff Girls fanfic, you could have a plot where Blossom, Bubbles, and Buttercup are shrunk down to microscopic size. They then have to navigate through the body of a Townsville citizen who has been infected by a strange virus. Along the way, they learn about the inner workings of the human body and also have to fight off the virus from the inside. Another idea is that a powerful wizard casts a spell on Townsville that makes everyone forget who the Powerpuff Girls are. The girls have to find a way to break the spell while also dealing with the chaos that erupts in the city without their reputation to back them up. One more plot could be that a mysterious force is causing all the animals in Townsville to become super - intelligent and start rebelling against humans. The Powerpuff Girls have to find a balance between protecting the humans and understanding the animals' grievances.
A cool plot idea for a Power puff Girls fanfic could be that a new villain emerges who has the ability to create clones of the Powerpuff Girls. These clones start causing chaos in Townsville, and the real girls have to find a way to distinguish themselves from the clones and defeat the villain. Or perhaps there could be a story where the girls enter a parallel universe where everything is opposite. They are the villains there, and they have to figure out how to get back to their own universe while also dealing with their 'evil' counterparts. Also, a plot where they team up with other superheroes from different shows to fight a common mega - villain would be really exciting.
One idea could be a time - travel plot. The Powerpuff Girls travel back in time to when the Professor was a kid and help him deal with bullies. This would show a different side of their relationship and also give room for some fun adventures in the past. Another plot could be an alien invasion where the aliens have a new type of power that the girls have to figure out how to counter. It could involve some scientific exploration on their part. Maybe a third plot could be a situation where the girls lose their powers temporarily and have to rely on their wits and teamwork more than ever to save Townsville.