One idea could be a Metroid crossover with the Legend of Zelda. Samus could find herself in Hyrule, facing off against Ganon's forces while also dealing with Metroids that have somehow made their way there. Another idea is a crossover with the Mega Man series. Samus and Mega Man could team up to take on a new threat created by Dr. Wily and the Space Pirates combined.
First, decide which universe you want to crossover with Metroid. For example, if it's the Halo universe, think about how the technology and species from both would interact. Then, create a plot that brings the main characters together. Maybe Master Chief and Samus are forced to team up against a common enemy. Start with a strong opening scene that sets the tone, like Samus receiving a distress signal from a Halo - like planet.
Power - up and evolution is also a common theme. In the Metroid series, Samus has different power - ups and her suit evolves. In Naruto, the characters grow in power through training and new jutsu. In crossovers, often Naruto will experience something like a power - up similar to Samus' suit upgrades, or Samus might learn about the concept of chakra and use it in a new way, which ties into this theme of power - up and evolution.
In Metroid fanfic, a common and great storyline is Samus getting stranded on an unknown planet filled with dangerous and unique creatures. She has to use her skills and the limited resources she has to survive and find a way off the planet. Another good one is when there are alternate timelines. For example, what if Samus didn't destroy the Metroids as she did in the main storyline? This can lead to a whole new set of adventures and challenges for her. Some fanfics also explore Samus's emotional side more, like how she deals with the loneliness of her job, which is quite interesting.
First, you should study the Metroid universe. Know the characters like Samus, the different types of Metroids, and the planets. Then, come up with an interesting concept. It could be a new adventure for Samus or a different take on an existing event. Next, create some engaging characters, whether they are new or existing ones with a different spin. Don't forget to write in a way that keeps the action and adventure elements that are characteristic of Metroid.
In such a fanfiction, the story could be set in a new, unexplored part of space that is somehow connected to both the Star Fox and Metroid universes. Samus could be on a mission to investigate this area when she runs into the Star Fox team. They initially have some misunderstandings due to their different ways of operating, but eventually, they realize they need to work together. The plot could include epic space battles, exploration of ancient ruins filled with secrets related to both franchises, and character development as they learn from each other's skills and experiences.
A cool concept in Metroid Prime crossover fanfiction is the combination of different power - up systems. For instance, if Samus were to cross over with a game like Ratchet & Clank, she might get access to some of their wacky and powerful weapons, while they could get a taste of her Morph Ball ability. It could also be interesting to see a crossover where Samus meets characters from the Mass Effect universe. They could exchange technology and knowledge, and Samus could learn about biotics while sharing her knowledge of Chozo technology.
One popular 'Metroid fanfic' story could be about Samus's early adventures before the events in the official games. For example, it might explore her training and how she first encountered the Metroids. Another could be a story that focuses on the relationship between Samus and the Chozo, delving into their history together. There are also 'Metroid fanfic' that reimagine the Metroid universe with different power - up systems for Samus.
Obviously, Fox McCloud from Star Fox would be a main character. He's the leader of the Star Fox team and a skilled pilot. And Samus Aran from Metroid is a must - have main character too. She's a badass bounty hunter with amazing combat and exploration skills.
One interesting concept could be the combination of Mega Man's robotic abilities and Samus' exploration skills. For example, Mega Man might use his arm cannon in the more maze - like environments typical of Metroid games. Another concept could be the meeting of their respective villains. Dr. Wily and the Space Pirates could form an alliance, creating a greater threat for the heroes to overcome.