Another concept could be that an alien force brainwashes Mega Man to use his powers for their own evil purposes. The fanfic could then be about his journey to break free from the alien control and save the world from their plans. This could involve him having to overcome not only the physical restraints of the brainwashing but also the mental conditioning.
Dr. Wily would be a classic choice. He has the intelligence and the motive to brainwash Mega Man. He could use Mega Man's power to take over the world or defeat his other enemies.
One plot idea could be that the Virus X starts to infect the digital world in unexpected ways, causing glitches in the Megaman universe. For example, it could make some of the usual power - ups work in reverse. Another idea is that a new character is created as a result of the Virus X's influence and has to choose between helping the Virus or fighting against it. And a third plot idea might be that the Virus X targets Megaman's closest allies, forcing him to go on a rescue mission while also trying to find a cure for the infected.
One idea could be a crossover with Sonic. Imagine Megaman and Sonic teaming up to stop a new villain who is causing chaos in both their worlds. They could combine their unique abilities, like Megaman's weapon switching and Sonic's super speed.
A 'megaman x crossover fanfic' could involve a crossover with the Pokemon universe. X could end up in the Pokemon world and have to work with a trainer and their Pokemon to stop an evil organization that is using technology to harm Pokemon. He could use his weaponry to help in battles against the organization's powerful machines.
One idea could be that Megaman X and Nana team up to fight a new powerful enemy that threatens their world. They could combine their unique abilities to overcome various obstacles during the battle.
One idea could be to cross Megaman Zero with another popular game series like Sonic. Imagine Zero running at high speeds through the colorful zones in Sonic's world. Another idea is to cross him with a Final Fantasy world. Zero could be a mysterious warrior in that RPG setting, using his skills to fight against the powerful summons and magic - users there. Also, a crossover with the Metroid series would be cool. Zero exploring the desolate planets and facing off against the space - pirates and Metroids could make for an exciting fanfic.
One idea could be to explore an alternate universe where the characters have different powers. For example, Geo could have the power to control time instead of EM waves. Another idea is to focus on a new villain that is more powerful and complex than the ones in the original. This villain could have a backstory that makes the readers sympathize with them a bit. Also, a fanfic could be about the characters' daily lives outside of their battles, like Geo's school life and how his friends interact with him there.
One idea could be a crossover where Naruto characters gain the abilities of Megaman Zero. For example, Naruto could have Zero's saber and use it in his battles. Another idea is to set the story in a post - apocalyptic world like in Megaman Zero, but with Naruto characters trying to survive and restore peace. Maybe Sasuke could take on a role similar to Zero, being a lone warrior at first but then joining forces with others.
One idea could be a story where Bass and Roll are forced to team up to face a new, powerful enemy that neither could defeat alone. They start off distrusting each other but gradually learn to work together and respect one another's skills.
One idea could be that Mega Man and X team up to face a new, extremely powerful enemy that neither could defeat alone. For example, a virus that can adapt to their attacks instantly.