One idea could be a crossover with Godzilla. Mothra could team up with Godzilla to fight a new, more powerful alien monster that has invaded Earth. Their combined powers would create epic battle scenes.
A crossover with the Avengers in the Marvel universe. Mothra could be seen as a powerful ally, perhaps using its wings to create strong winds to help the Avengers during a battle against a villain who controls the elements.
Maybe in the fanfiction, there's a powerful force threatening their world. Godzilla and Mothra have to combine their powers. During this process, they start to understand each other on a deeper level. Their relationship could be shown through small gestures like Godzilla protecting Mothra from a surprise attack, and this could lead to a more intimate connection as the story progresses.
One idea could be a human scientist who discovers a way to communicate with Mothra and tries to convince her to team up with Godzilla against a new common enemy, like an alien invasion. The scientist could be in a race against time as the world is being quickly overrun.
One idea could be a character from the Enclave finding themselves in a situation where they have to team up with a group from the Fallout world they usually oppose. Maybe a lone Enclave soldier gets separated from his unit and is forced to rely on a group of wastelanders to survive. This could lead to a lot of character development as he sees a different side of the world outside the Enclave's ideology.
A plot could revolve around the two monsters being outcasts in their own ways. Godzilla is often seen as a destroyer, and Mothra is a more benevolent but still a strange creature. They find solace in each other. Their love story could involve them trying to convince the other monsters and the humans that they are not a threat when they are together, and that their union can bring about positive change. They could start by protecting a small island together and slowly gain the trust of others.
One idea could be that the Turtles from 1987 end up in the 2003 universe and have to adapt to the darker and more serious tone. They could team up with the 2003 Turtles to fight a common enemy like the Shredder. The 1987 Turtles' more light - hearted and comical ways might initially clash with the 2003 Turtles' brooding nature, but they eventually learn from each other.
One idea could be a crossover with Undertale. The characters from Glitchtale could interact with the original Undertale characters in a new and unexpected way. For example, Betty from Glitchtale could team up with Chara from Undertale for some sort of dark plan. Another plot could involve a crossover with a different game like Minecraft. The Glitchtale characters could find themselves in a blocky world, having to adapt to new rules and enemies. Maybe Sans from Glitchtale could use his powers in the Minecraft world in a really creative way.
A great plot idea would be Android 21 crossing into a world where technology is feared. She'd have to prove that not all advanced technology is bad. Also, she could cross into a world of pirates, using her skills to navigate the high seas and fight off other pirates.
A plot idea could involve a magical crossover. Maybe a character from a magical fanfiction world accidentally enters the Wayside School. This could lead to chaos as the normal rules of the school are disrupted. The students might have to learn about magic to help the new character return home, and in the process, they gain some magical abilities themselves for a short time. This could also create new friendships and rivalries among the characters.
A Broly crossover with the Naruto universe could be really cool. Picture Broly in the Hidden Leaf Village, his incredible power causing quite a stir. Maybe he could get involved in the fight against the Akatsuki, using his brute strength in a world of ninjas. It would be interesting to see how he adapts to chakra and ninja techniques.
One idea could be a crossover with a zombie apocalypse-themed story. The undead elements from Sankarea could blend well in a world full of other zombies, creating new challenges for the characters. For example, Rea could use her unique undead state to her advantage in a different way than the regular zombies.