One possible plot could be that Luigi is kidnapped by a group of mischievous goombas who are being controlled by a powerful dark magic user. Luigi, while kidnapped, uses his wits to befriend some of the weaker goombas and gets them to help him send a message to Mario. Mario then has to figure out where Luigi is being held based on the clues in the message.
Maybe it's a new villain in the fanfiction. This villain could be after Luigi because he thinks Luigi has some sort of special power or knowledge. So the villain kidnaps Luigi in a very sneaky way, like using a magic spell to put Luigi to sleep first and then whisking him away to a secret lair hidden deep in a dark forest.
Yoshi could also be the rescuer. Yoshi has his long tongue that can be used to grab things from a distance. He could use it to pull Luigi out of a locked cage or something. And Yoshi is very fast and can jump high too. So he'd be a great candidate to go on a rescue mission for Luigi.
The kidnapper might be a deranged Toad. Maybe this Toad has been corrupted by some evil force and decides to kidnap Luigi for reasons only known to the twisted mind of this new 'evil Toad'.
Maybe there's a new villain in the kingdom who has a device that can transform enemies into harmless forms, like turning Luigi into a baby. The villain wants to use this to stop Luigi and Mario from interfering with his evil plans. Mario has to protect baby Luigi from the villain's minions while looking for a way to break the transformation. This could involve exploring new areas of the kingdom and meeting new characters who might have the knowledge to reverse it.
In a 'luigi turns into a girl' fanfiction, the plot might involve Luigi being transformed due to a strange experiment gone wrong in the Mushroom Kingdom's science lab. His new female form causes a stir among the inhabitants. He could struggle with how others perceive him now. For example, some characters might treat him differently. However, he also uses this opportunity to see the world from a different perspective and becomes more confident in himself over time.
Well, perhaps Luigi runs away because he's tired of living in Mario's shadow. He might decide to explore new lands on his own, meet new characters, and have adventures that are just about him, not always being the sidekick.
Well, perhaps it involves Luigi getting some strange illness that no one in the Mushroom Kingdom has seen before. So, Mario and Princess Peach have to search for a cure all over the place. They could meet new characters during their search who either help or hinder them in their quest to make Luigi well again.
Well, perhaps the plot could involve Daisy and Luigi facing the challenges of new parenthood. They might struggle to balance their own lives and duties while taking care of the baby. For example, Luigi could be worried about protecting the baby from the various threats in their world, while Daisy is focused on the baby's growth and development.
One possible plot could be that Luigi and Daisy discover they are going to have a baby. They then start preparing their home, like painting a nursery. Luigi might be a bit nervous but also excited, and Daisy could be the strong one, reassuring Luigi throughout the process.
Well, it could be a story full of love and adventure. Maybe Luigi has to overcome his shyness and prove to Daisy's family that he's worthy of her. They might go on a quest together before the wedding, like finding a special flower that is said to bring eternal love to their marriage.