A great plot could involve a new threat that is a combination of the dark forces from both universes. Naruto and Mario find themselves in a strange new dimension where the rules of both their worlds blend. They must learn to trust each other and combine their unique skills. For example, Mario's invincibility star could enhance Naruto's speed and strength during battles, and Naruto's sage mode could help him sense hidden traps in the Mushroom Kingdom like he does in his own world.
One interesting plot could be that Bowser teams up with the Octarians in the Splatoon world. He wants to use their ink technology to take over both the Mushroom Kingdom and the Splatoon world. Mario has to then form an alliance with the inklings. He travels through different ink - filled levels, learning new skills like swimming in ink and using ink - based weapons. Along the way, he discovers secrets about the connection between the two worlds. They finally face Bowser and the Octarian leader in a huge battle where Mario combines his classic moves with the ink - powered attacks of the inklings to save both worlds.
Maybe the Mushroom Kingdom is in trouble. A strange magical force is draining all the power - ups. Mario discovers that this force is linked to Equestria. He travels there and meets Rarity. Rarity is impressed by Mario's unique style and decides to help him. They find out that a corrupted magic crystal in Equestria is causing the problem. So they have to find a way to purify the crystal. Along the way, they face many challenges, like dealing with jealous unicorns who don't want an outsider like Mario interfering in their world.
One possible plot could be that Mario and Kirby's worlds are somehow merged due to a powerful villain's spell. They have to team up to find the source of the spell and break it. Along the way, Mario could use his jumping and power - up skills while Kirby uses his ability to copy enemies' powers. They might encounter challenges like a new type of Goomba that can fly like some of Kirby's foes.
Well, perhaps Bowser somehow makes a deal with some of the more malevolent characters in the Undertale world, like Flowey. Then Mario has to not only deal with Bowser but also the new threats from the Undertale realm. He might have to learn about the concept of LOVE and EXP in the Undertale world to fully understand how to defeat his enemies. And along the way, he could meet Sans and Papyrus, and they could have some really funny exchanges due to their very different personalities.
One possible plot could be that Mario and Luigi are exploring a new world and accidentally stumble upon the Pokemon world. They team up with Ash and Pikachu to stop Bowser who has teamed up with Team Rocket to steal all the Pokeballs and use the Pokemon's power to take over both the Mushroom Kingdom and the Pokemon world.
A really creative one is 'Naruto and Mario: The Fusion Quest'. This fanfiction has a magical device that fuses Naruto and Mario into one being. This new entity has to use the combined powers of both to stop an ancient evil that threatens both the Mushroom Kingdom and the Hidden Leaf Village. It's a wild concept that makes for an exciting read.
Imagine that Michael Rosen is from a parallel dimension where everything is made of words. When he enters Mario's world, he starts to turn the enemies into harmless words. Bowser, seeing this as a threat, tries to stop him. Mario and Michael team up. Michael uses his word - changing ability to weaken Bowser, and Mario gives the final blow. In the end, they learn from each other and Michael returns to his word - dimension, but not before leaving behind some magical word - seeds that grow into beautiful story - trees in the Mushroom Kingdom.
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 Sonic have to team up to save both their worlds from a new, powerful villain that is threatening to merge their dimensions in a chaotic way. For example, Bowser and Dr. Eggman could accidentally awaken an ancient evil while arguing over who is the better baddie.
Well, a cool plot for Mario Sonic crossover fanfiction might involve a new character that can travel between their worlds freely and is causing chaos. Mario and Sonic initially suspect each other but then realize they need to join forces. For example, this character could be stealing power - ups from Mario's world and Chaos Emeralds from Sonic's world to gain ultimate power. They would have to explore both worlds, facing their respective villains' minions along the way.