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.
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.
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 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.
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.
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.
Once upon a time, Mario found himself in the magical world of MLP. He was quite confused at first, with all the colorful ponies and floating castles. But being the brave hero he is, he decided to explore. He met Twilight Sparkle, who was intrigued by this strange new being. Mario showed her his jumping skills, and Twilight was amazed. They then went on an adventure together to find a way to send Mario back to his world, facing all kinds of challenges along the way, from evil magic spells to tricky terrains.
Maybe the Avengers are shrunk down to the size of ponies and end up in Equestria. They have to adapt to the new world and its rules. Iron Man could try to build new tech using Equestrian resources, and Captain America could use his leadership skills to form an alliance with the ponies against a common threat, like a dark magic - based enemy that wants to take over both worlds.
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 the Autobots find themselves in Equestria due to a space - time rift. They team up with the ponies to fight a common enemy like a new breed of Decepticons who are after the magical energy in Equestria. The ponies could use their magic to help the Autobots repair and upgrade, while the Autobots offer their advanced technology to protect Equestria.
Maybe there could be a Creepypasta entity that invades Equestria. Let's say a well - known Creepypasta character like Slenderman appears in Ponyville. The ponies are initially confused and then terrified as they start to notice strange things happening. The MLP characters then have to figure out how to get rid of this intruder and restore peace to their land. It could be a story about how the kindness and friendship of the ponies are put to the test against the malevolence of Creepypasta.