Another idea is that the Dragon Balls are discovered in the My Hero Academia world. Different factions in the My Hero Academia universe start competing to gather the Dragon Balls. This could lead to some unlikely alliances between heroes and villains as they all have their own reasons for wanting to make a wish with the Dragon Balls. The Dragon Ball characters could also be summoned by accident through the wish - making process, and then they get involved in the chaos of the My Hero Academia world.
A cool plot could be a training arc where the characters from My Hero Academia train with the Dragon Ball characters. Izuku could train with Gohan, learning about ki control and how to better use his power. Meanwhile, the Dragon Ball characters could learn about the importance of strategy in combat from the My Hero Academia heroes. And then, they could face a new villain that requires both their skills and powers combined to defeat.
One possible plot could be that the characters from My Hero Academia are suddenly transported to the world of Blue Exorcist. They have to team up with the exorcists there to fight a new common enemy that has powers similar to the quirks in My Hero Academia but also has demonic abilities. For example, Izuku could learn some exorcist techniques from Rin and use his quirk in new and creative ways to combat this threat.
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 interesting crossover could be the characters from My Hero Academia having to face the power levels of Dragon Ball characters. For example, Deku might learn from Goku about the concept of constantly pushing one's limits and training harder. Another could be the quirks in My Hero Academia being combined with the ki abilities of Dragon Ball. Maybe Todoroki's ice and fire quirks could be enhanced with the use of ki control.
A cool plot could be that Godzilla is actually an ancient being that was sealed away long ago in the My Hero Academia world. Due to some villainous activity, the seal is broken. Now, the heroes not only have to deal with the immediate threat of Godzilla but also figure out how to reseal it. There could be a sub - plot where a young hero discovers an old prophecy about Godzilla and has to convince the others that it's real and relevant to their current situation.
One idea could be that the Pokemon world has some sort of villainous force that is affecting the balance of power, similar to the villains in My Hero Academia. The heroes from My Hero Academia are transported to the Pokemon world to help. They could team up with Pokemon trainers and use their quirks in combination with Pokemon attacks to fight against the common enemy.
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 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.
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, 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.