One idea could be that Fluttershy discovers Tails' mechanical skills and they work together to build a special sanctuary for injured animals in both their worlds. This would combine Fluttershy's love for animals and Tails' engineering prowess.
Maybe Tails gets lost in Fluttershy's world. Fluttershy then takes it upon herself to help him find his way back. Along the way, Tails learns about the magic and different creatures in her world, and Fluttershy learns about his technology. It could be a story of cross - world friendship and discovery.
Maybe the tree is sick, and Fluttershy, with her love for all living things, tries everything she can to heal it. She spends days and nights by the tree, singing to it, bringing it water, and asking other forest animals for help. In the process, she uncovers a mystery about the tree's origin that has been long forgotten in the pony world.
Maybe in the fanfiction, the three - tailed beast crosses over into a modern - day human world. People initially fear it, but then they discover that it has a gentle side and is actually trying to find its way back home. It could form a bond with a group of humans who help it on its journey, leading to many adventures along the way.
One idea could be exploring the origin of the Ten - Tails in a different light. Maybe it was created by an ancient civilization for a noble purpose that got corrupted over time. Another could be a story where a young ninja discovers a hidden power within the Ten - Tails and has to learn to control it without being consumed by its dark energy.
Another plot could be Tails getting lost in a dimension where all the laws of physics are different. His gadgets don't work as expected, and he has to rely on his wits and basic survival skills. He could meet some new friends or foes in this dimension and try to find his way back home while also learning about this strange new place.
One idea could be that Luigi and Tails team up to solve a mystery in a strange, hybrid world that combines elements from their respective universes. They could use Tails' mechanical skills and Luigi's courage to face unknown challenges.
One idea could be a crossover where Naruto visits Equestria and meets Fluttershy. He could learn about her kindness towards animals and they could team up to protect the magical creatures there from some sort of threat. Another could be a story where Fluttershy somehow gets transported to the Naruto world and has to adapt to the more dangerous environment, while Naruto helps her understand the ways of his world.
Another plot could involve the daughter going on a journey to learn more about her parents' past. Along the way, she meets different characters who knew Tails and Cosmo. This journey of self - discovery also helps her to understand her own place in the world and her unique abilities.
One idea could be that Cosmo and Tails work together to build a new type of spaceship. They use their combined knowledge of mechanics and botany. Cosmo might contribute with her understanding of plant - based energy sources, while Tails uses his engineering skills. Another plot could involve them exploring a mysterious new planet where they encounter strange creatures. Cosmo could communicate with the planet's plant - like life forms, and Tails would figure out how to navigate the terrain.
Perhaps in the fanfiction, the Zero Tails is a manifestation of the negative emotions of the ninja world as a whole. A group of young ninjas discover this and they try to find a way to purify the Zero Tails. They seek the help of old sages and learn ancient jutsu to attempt this purification, which could lead to a battle against those who want to keep the Zero Tails as a weapon of mass destruction.
One idea could be Naruto having a unique connection with the Nine Tails that allows him to access new forms not in the original series. For example, a form that combines his human features with more fox - like aspects in a more aesthetically pleasing and powerful way.