Perhaps in the fanfic, there could be a villain who is trying to steal the cutie marks of the ponies in the MLP world and use their power for evil in the My Hero Academia world. The heroes from both universes would then have to team up. Deku could use his One For All to protect the ponies, while the ponies could use their friendship magic to support the heroes in combat.
One idea could be to explore the backstory of a minor character. For example, what was the life of a random student in Class 1 - B like before coming to U.A. High? Another could be a 'what if' scenario, like what if Izuku Midoriya didn't get One For All. Maybe he'd develop his own unique quirk through sheer determination and hard work. Or a fanfic could focus on the villains' side, showing how they came to be and their motives in more depth.
First, choose the characters from both universes carefully. Decide which ones will interact and how. For example, you could start with Bakugo from My Hero Academia ending up in New York City from the Marvel universe. Then, create a conflict. Maybe a villain from Marvel, like Loki, is causing trouble and Bakugo's explosive quirk can be both a problem and a solution in this new world. Don't forget to add some character development. Bakugo could learn about teamwork from the Avengers, which is something he struggles with in his own world.
One interesting plot could be that a Prototype character, say Mercer, somehow gets his powers transferred to a My Hero Academia villain. This villain then becomes extremely powerful and starts causing chaos in a way that the heroes can't handle. The heroes have to figure out how to stop a foe that can shape - shift, regenerate, and has superhuman strength. They seek help from the Prototype world, and a character from there has to work with the heroes to find a way to reverse the power transfer or at least find a weakness in the empowered villain.
Well, the plot could involve a quirk experiment gone wrong that creates portals between the two universes. The Avengers and the MHA heroes end up on the wrong sides. At first, there's a lot of misunderstanding and fighting between them. But then they realize that there's a bigger threat behind all this chaos. For instance, Loki could be working with a MHA villain to take over both worlds. The Avengers and the MHA heroes then have to put aside their differences and work together to stop this evil plan. The story could explore how different powers interact and how characters from two very different universes grow to respect and rely on each other.
One possible plot could be that Naruto somehow gets transported to the world of My Hero Academia. He could be mistaken for a new type of Quirk user at first. Maybe he tries to understand their system of heroes and villains while also showing off his ninja skills, which would be really unique in that world. And he could end up teaming with some of the My Hero Academia characters to fight a common enemy that threatens both worlds.
One possible plot could be that the villains in My Hero Academia somehow get their hands on the Infinity Stones. They could use the power of the stones to start warping reality. For example, they might use the Reality Stone to make the heroes' quirks ineffective or change the very nature of the hero society. The heroes would then have to band together, not just from UA but from all over the world, to try and stop the villains from completely taking over. They would need to figure out how to combat the power of the Infinity Stones, perhaps by finding some sort of counter - quirk or ancient hero relic.
Well, for example, Bakugo's explosive personality might be toned down a bit in the MLP world. He could still be hot - tempered but also learn about friendship and kindness from the ponies. Midoriya would probably be even more eager to make friends and learn from the ponies' harmonious society. He might be seen as a bit of an oddball at first, but his kind heart would win the ponies over.
One idea could be exploring the backstories of the members of the Liberation Army in more detail. Maybe show how they came to join and their individual motives.
A great plot could involve Tsu going on a training journey outside of UA. She discovers a new aspect of her quirk during this journey. Like she finds out she can communicate with a certain type of animal that she previously couldn't. This new discovery then becomes crucial in a battle against a group of villains who are causing trouble in the area she's training in. She uses her newfound ability to gather intel and then defeat the villains.
One idea could be that Ladybug's Miraculous powers are somehow connected to a Quirk in the My Hero Academia world. For example, maybe her Lucky Charm ability could be seen as a very unique and unpredictable Quirk. Another plot could involve Ladybug and a My Hero Academia character teaming up to fight a common enemy that is causing chaos in both their worlds. This would require them to learn about each other's powers and work together in a way that combines the best of both universes.