You could write a Paper Mario fanfic that involves time travel. Mario goes back in time to prevent a great disaster that happened in the past of the Paper Mario world. This could lead to him interacting with past versions of characters and changing the course of history in unexpected ways. Or, a fanfic about a new villain that only exists in the paper realm and has unique powers that Mario has to figure out how to defeat.
One idea could be to create an alternate universe where the stickers have minds of their own and they form a rebellion against the characters who use them. It would add a whole new layer of conflict and adventure.
One idea could be a crossover with the Mario Kart universe. Mario and his friends from Super Paper Mario could find themselves on the race tracks, facing off against the regular Mario Kart characters. Another could be a crossover with the Legend of Zelda. Maybe Mario has to traverse Hyrule, using his paper - like abilities in a new and strange land filled with Zelda - style dungeons and puzzles.
Another interesting concept is that the harem is formed due to a magical accident. Mario has to figure out how to reverse it, but in the process, he discovers that each member of the harem has a hidden power or ability. So instead of just trying to get rid of the situation right away, he decides to work with them to solve a greater threat to the Paper Mario world. The fanfiction could then detail their journey and the growth of their relationships.
Well, you could write a fanfiction where Mario gets trapped in a world made entirely of stickers. He has to find a way to break free by solving various puzzles using only the stickers he can find. Or perhaps a story about a villain who is stealing all the rare and powerful stickers, and Mario has to stop him while also learning about the villain's backstory which led to this evil plan.
One idea could be that Naruto gets transported to the Mario world. He might use his ninja skills to help Mario and Luigi in their battles against Bowser. For example, Naruto could use his Shadow Clone Jutsu to confuse Bowser's minions while Mario goes for the power - up.
One idea could be a racing tournament where Mario and Sonic team up against some new, powerful villains. They have to combine their unique skills, like Mario's jumping and Sonic's speed, to overcome the challenges of the track which is filled with traps from both of their worlds.
One idea could be a story where Mario and Lemon (assuming it's a character) go on an adventure through a new and mysterious world in the Mushroom Kingdom. They could encounter new enemies and have to use their unique skills to overcome challenges.
There are fanfictions where the villains from the Paper Mario series get a backstory makeover. For instance, a story might explore Bowser's childhood and what led him to become the power - hungry villain he is. It could show his insecurities and how his experiences shaped his actions, which would add a whole new layer of depth to his character in the fanfiction world.
One idea could be a racing tournament where Mario, Sonic and their friends compete. It would be a high - speed adventure with crazy power - ups from both universes. Maybe Mario could use a Sonic - inspired speed boost item, and Sonic could try out a mushroom to grow big for a short time.
One idea could be that Pauline gets kidnapped by Bowser and Mario has to go on an extra challenging adventure to save her. He might face new types of enemies and obstacles along the way.