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.
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 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.
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.
A plot idea could be that Naruto discovers a new, ancient form of chakra that has been lost for centuries. He then has to train to master this chakra while also dealing with the political implications within the Hidden Leaf Village. Some elders might be against him exploring this new power for fear of the unknown, but Naruto, being Naruto, is determined to master it for the good of the village.
One idea could be that the events of 9/11 somehow influence the Hidden Leaf Village. For example, they might tighten security and Naruto could be part of a new team in charge of protecting the village from potential outside threats inspired by the real - world event. Another plot could involve characters from Naruto trying to understand the concept of such a large - scale tragedy and how they can prevent similar things in their own world.
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.
One idea could be that Neji discovers a new hidden power within Naruto that he helps Naruto master. This could lead to them having to face a new, powerful enemy together.
One interesting plot idea could be a time - travel story. For example, Naruto is sent back in time to the era of the First Hokage. He could use his knowledge of future jutsu and events to change things for the better in the past. Another idea is a story where Naruto discovers a hidden clan within Konoha that has a unique and powerful Kekkei Genkai. He then has to help this clan gain acceptance in the village. A third idea might be a story where Naruto is turned into a different creature, like a cat or a fox, and has to find a way to turn back while still dealing with the normal threats to the village.
One idea could be that the reincarnated character has knowledge of future events in the Naruto world. For example, they know about the Akatsuki's true intentions from the start and can start preparing the Hidden Leaf Village earlier. Another plot could be that they have a special power from their past life that no one in the Naruto world has seen before, like the ability to control modern technology within the ninja world. A third idea is that they are reincarnated as a side character and their actions end up changing the entire course of the original Naruto story in unexpected ways.