Perhaps the fanfiction could explore a future where quirks start to disappear. This would create a huge crisis in the hero society. The remaining heroes would have to find a way to either stop the disappearance or redefine what it means to be a hero without quirks.
One possible plotline could be about the next generation of heroes. Maybe the children of the current heroes are starting their own hero journey at UA High. They might face new villains with even more complex quirks.
One interesting plotline could be Deku facing a new, extremely powerful villain that challenges his understanding of heroism. Maybe this villain has a quirk that can nullify all other quirks, forcing Deku to rely on his wits and physical training rather than just his One For All power.
One possible plotline could be that Naruto mistakes a character from My Hero Academia as a threat to the ninja world. So, he banishes them to prevent any potential harm. For example, if he sees a powerful quirk user like All Might in the wrong context, he might think they are a new kind of enemy.
It could be Deku's son or daughter. They would inherit some of his amazing quirk, but also face the pressure of living up to their father's legacy. They would have to carve their own path in the hero world.
Another possibility is that the fanfiction explores the powers of the characters in a new light. Since they are in a different time period, they might have to use their quirks in unexpected ways. Maybe some quirks are more or less effective in the past compared to the present, and this creates new challenges and strategies for the heroes as they try to change the future.
One possible plotline could be a tournament - style event where characters from Naruto and My Hero Academia compete against each other. This would allow for exciting battles as the different powers and abilities are pitted against one another. For example, Naruto's shadow clone jutsu against Bakugo's explosions.
One interesting plotline could be a hero sacrificing themselves in a major battle against a powerful villain. This would have a huge impact on the other characters, like how Midoriya might be inspired to become even stronger in memory of the fallen hero.
The deaf hero might be highly observant. Since they can't rely fully on sound, they would have to be really good at noticing visual cues. For example, they could be very perceptive of body language, which could be useful in battles or social interactions.
One possible plot could be that Naruto is somehow transported to the My Hero Academia universe. He meets Midnight and they team up to train students in a new, combined style of combat that incorporates Naruto's ninja skills and the quirks of the My Hero Academia world.
One idea for a crossover is the sharing of values. The Avengers stand for justice and protecting the world, and the heroes in My Hero Academia also have a strong sense of justice. They could come together to fight a common enemy that threatens both their universes. Maybe the Avengers could introduce some new combat techniques to the My Hero Academia heroes, and in return, the My Hero Academia characters could show the Avengers some unique ways of using their quirks in combat.
In this fanfiction, the Flood might return in a more evolved and dangerous form. The story could revolve around the efforts of the protagonists to not only stop the Flood's spread but also to find a more permanent solution to this ancient menace. They might have to explore long - forgotten Forerunner technology or even make unthinkable sacrifices.