One idea could be a crossover adventure where Megaman X and Samus team up to fight a common enemy that threatens both of their worlds. They could start off as rivals, not trusting each other's methods at first, but as they face challenges together, they learn to respect and rely on one another.
A possible plot twist could be that one of them is actually being controlled by the enemy without the other knowing. For example, Megaman X might be unknowingly following the commands of a powerful virus that is trying to use him to get to Samus and her advanced technology. This would create a lot of tension and drama as Samus has to figure out what's wrong with X and try to free him without getting killed.
Well, 'A Bond Beyond Worlds' is also a popular one. It delves deep into how Megaman's digital world and Samus's more physical, alien - filled world can intersect. Their different abilities and personalities play a key role in the story. For example, Megaman's logical thinking and Samus's survival instincts create an interesting dynamic as they start to fall in love. There are some really cool action scenes in this fanfiction too that tie in with the romantic plot.
You can start by looking on popular fanfiction websites like Archive of Our Own (AO3). It has a large collection of fanfictions from various fandoms, and you're likely to find some good ones about Megaman and Samus there.
One popular fanfiction might be those that explore the relationship between the original Megaman and Megaman X in different timelines. For example, a story could focus on how X was created based on the original Megaman's design, and how their powers and abilities compare and contrast.
One common theme is the battle between light and dark. Samus represents the light side, being a bounty hunter who fights for good in the Metroid universe, while Dark Samus is, as the name suggests, the dark counterpart. Their relationship in fanfiction often explores this contrast.
Dr. Wily could be the main villain. He might have found a way to travel through time or dimensions to the world of Mega Man X. He then uses his knowledge of Mega Man's weaknesses and combines it with new technology in the Mega Man X world to create even more powerful and devious robots.
Perhaps in the fanfiction, Mega Man and Mega Man X meet in a virtual world created by a mad scientist. The virtual world is filled with distorted versions of their old enemies. They have to work together to find the core of this virtual world and shut it down. Along the way, they share their experiences and upgrade each other's abilities, leading to a new and more powerful form for both of them when they finally face the scientist.
It contributes by expanding the lore. Fanfictions can create new backstories for Protoman and Megaman, filling in gaps that the official games might not have covered. For example, their relationship before a certain event in the game timeline can be explored.
There could be epic battles. Maybe the characters from Megaman Starforce and Megaman X would team up to fight a powerful common enemy. They might combine their unique abilities, like the Starforce's EM Wave powers and X's advanced weaponry.