One idea could be that baby Mario and baby Luigi get lost in a magical forest filled with strange creatures. They have to use their baby wits and little jumps to get through obstacles and find their way back home. Maybe they befriend a little fairy who guides them part of the way.
One idea could be that Baby Mario and Baby Peach go on a magical adventure through the Mushroom Kingdom, encountering new and strange creatures along the way. They might have to work together to solve puzzles to reach a special power - up that can save the kingdom from a new threat.
A really fun 'baby daisy and baby luigi fanfiction' could be set in a world of toys. They are toys themselves and they have to work together to escape from the clutches of an evil toy collector. They make friends with other toys along the way and use their unique skills, like baby Daisy's ability to find hidden paths and baby Luigi's courage, to overcome the challenges.
One idea could be that Mario and Peach's baby has special powers inherited from both of them. For example, the baby could have Mario's jumping ability and Peach's ability to communicate with nature. This would lead to all sorts of adventures as the baby discovers its powers while growing up in the Mushroom Kingdom.
One idea could be that Mario and Luigi find a magical lemon tree in a hidden part of the Mushroom Kingdom. The lemons from this tree have special powers that they have to figure out how to use to save the kingdom from a new villain. For example, the lemons might give them temporary super strength or the ability to fly. Another plot could involve Luigi accidentally getting lost in a lemon - themed dimension while trying to find a rare ingredient for a recipe. Mario then has to brave this strange new world filled with lemon - based creatures to rescue his brother.
One idea could be that Mario and Luigi get transported to a strange new world where the rules of their own world are all mixed up. They have to use their combined skills in a whole new way to find their way back home. For example, Luigi might have to be more brave and take the lead in some situations while Mario has to use his speed in different ways than he's used to.
One idea could be that Mario and Luigi find a magical world that only they can enter together. In this world, they have to solve puzzles that require their unique skills as a team. For example, Mario's jumping ability and Luigi's higher jump and ability to float a bit could be combined to reach new heights and unlock secrets.
A plot could involve a new villain that infects Bowser's body and Mario and Luigi have to go inside to fight the source of the infection. Along the way, they learn about Bowser's past and his insecurities. This could lead to a change in their relationship with Bowser, from just enemies to something more complex like reluctant allies, as they all have a common goal to get rid of the new threat.
One interesting plot could be baby Naruto and baby Sasuke getting lost in the forest together. They have to rely on their budding instincts and nascent chakra to find their way back. Maybe they encounter some small, friendly forest creatures that help them. Another idea is that they accidentally switch places in the village for a day. This leads to chaos as the villagers react differently to them being in the wrong 'homes'.
Yoshi is a really popular character to include. He can be like a big brother figure to the baby Mario and baby Luigi. He could carry them around on his back and help them reach high places or cross dangerous areas.
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.