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, it could be about the heroes from My Hero Academia getting caught up in the events of Infinity War. Maybe Thanos targets the quirks in the MHA universe. Deku might try to use his One For All to stop Thanos, seeing it as a great evil. And the Avengers could be confused by the existence of quirks at first.
Another plot could involve a powerful and mysterious quirk user emerging who has the ability to control minds. This person starts to manipulate heroes into believing that other heroes are traitors. As a result, paranoia spreads throughout the hero community, and a civil war breaks out. The fanfic could then focus on how the students and unaffected heroes try to uncover the truth behind this mind - controlling quirk user and stop the civil war before it's too late. Along the way, there would be intense battles between heroes who were once friends, with each side believing they are in the right.
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 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.
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 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.
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.
One possible plot could be Sans using his teleportation ability (from his original game) in the My Hero Academia world to outwit villains during a big battle. For example, he could suddenly appear behind a villain like Stain and disarm him before he even realizes what's happening.
One possible plot could be that a powerful villain manages to release a virus that turns most of the population into mindless, powerful mutants. The remaining heroes, including the students of UA, have to not only fight these mutants but also find a cure. Deku could be leading the group, trying to figure out how to use his new powers in this chaotic situation.