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.
Definitely Izuku Midoriya. He's the main protagonist in the original series, so he would probably play a crucial role in any 'Days of Future Past' type of story. He could be the one leading the charge to change the future.
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.
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.
She could be influenced by a villain's ideology. For instance, if she was convinced that the current hero system is unfair and only benefits the strong. She might start to target heroes who she thinks abuse their power. Using her quirk, she'd be a formidable foe as she can manipulate gravity around objects and people.
Well, the plot could start with Todoroki suddenly realizing he has vampiric traits. Maybe he wakes up one day with a craving for blood. He tries to keep it a secret from everyone at the academy, but his performance in hero training starts to be affected. He becomes weaker in the daylight and stronger at night.
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.
In a 'My Hero Academia Noumu Deku' fanfiction, the plot could involve Deku being turned into a Noumu - like creature against his will. This transformation could lead to him being shunned by society at first. However, he could use his newfound strength, along with his unwavering hero spirit, to prove that he's still a hero at heart. He might team up with some unlikely allies, like villains who also oppose the unethical experiments that created him.
One possible plot could be Deku facing a villain who has the ability to manipulate air or oxygen levels. Deku has to use his quick thinking and newfound control over One For All in a low - oxygen environment. Maybe he discovers a new aspect of his power that allows him to function better on less oxygen.
Well, in a Deku kidnapped fanfiction, perhaps an anti - hero group kidnaps him. They might see Deku as a symbol of the hero system they oppose. They could hold him hostage to make demands on the hero society, like changes in how heroes are regulated. Or it could be a rival from his school days who is jealous of Deku's success and kidnaps him out of envy.