There could be a plot where Samus is sent to the Zelda universe to investigate some strange energy readings. There, she meets Link, and they initially distrust each other. But as they face various challenges together, like fighting off hordes of monsters and solving ancient puzzles, they grow closer. Another idea is that a group of interdimensional thieves steal something important from both Link and Samus. So, they have to work together to track down these thieves across different dimensions.
One idea could be that the male reader is a scientist who helps Samus understand some ancient technology she discovers during her adventures. Their relationship could start as a professional one and gradually develop into a deeper friendship or even a romantic relationship as they face various challenges together.
One idea could be a story where Samus gets lost in Zelda's world and Zelda helps her find her way back home. Along the way, they discover new places and secrets in Zelda's world. Another could be that they are both summoned to a mysterious realm and have to work together to escape. They use their different abilities, like Samus' combat skills and Zelda's magic, to overcome obstacles.
One idea could be a crossover adventure where Sonic and Samus team up to stop a powerful, universe - threatening villain. They could combine their unique abilities, like Sonic's speed and Samus' combat skills and advanced weaponry.
Perhaps in the fanfiction, Samus is on a mission to retrieve a powerful and corrupted video game cartridge. This cartridge is causing glitches in the entire gaming universe. AVGN, being the self - proclaimed video game expert, joins her. Along the way, they have humorous exchanges as Samus tries to understand AVGN's strange references to retro games and bad game design.
Well, for a Naruto and Samus fanfiction, perhaps a plot where Naruto is on a mission in an unknown realm and he meets Samus. They initially don't trust each other but soon realize they share a common goal of stopping a powerful, dark force that is spreading chaos in that realm. Or, Samus could be in search of a powerful energy source which she discovers is related to chakra in the Naruto world. And then there's the idea of a training arc where Samus teaches Naruto some of her combat skills and Naruto teaches her about ninjutsu.
Well, it could be about Samus exploring a new planet and coming across a Charizard. They initially see each other as threats but then realize they can help each other. Maybe Samus needs Charizard's fire power to defeat a powerful enemy on the planet, and Charizard needs Samus's technology to heal an injury.
A third plot could be that there is a tournament in a crossover universe where the best warriors from different dimensions are invited. Samus and Snake both enter, thinking they are the best in their own right. Initially, they are competitors, trying to outdo each other in the various challenges of the tournament. But as they face tougher opponents together, they realize that by teaming up, they have a better chance of winning. So they form an alliance and in the process, they develop a mutual admiration for each other's combat styles and strategic thinking.
The plot could center around a mystery. Maybe a strange phenomenon is occurring in both their worlds. Toon Link and Medli meet and start to investigate. They discover that an ancient evil from the past is trying to return. As they journey together, they learn more about each other's cultures and grow closer. Along the way, they face challenges like solving puzzles in ancient ruins and fighting off minions of the evil force.
You can start by looking on fanfiction websites like Archive of Our Own or FanFiction.net. These platforms have a wide variety of fanfics, and you can search specifically for 'Link x Samus' fanfics. Another option is to check out some Zelda or Metroid fan communities on social media platforms. Sometimes, fans will share their favorite fanfics or even write their own and post them there.
One idea could be a crossover where Naruto's world and the world of X - 23 from the X - Men collide. Maybe X - 23 is on a mission and accidentally ends up in the Hidden Leaf Village. She has to learn to adapt to this new place with its different culture and ninja ways. Naruto could be intrigued by her and her abilities, and they could team up to face a common enemy.