One idea could be that Rouge discovers some secret information about a powerful organization and Tails is wrongly accused of being a traitor when he tries to help her. So they have to work together to clear their names and expose the real villains behind the scheme.
A possible plot could be that a new villain uses mind - control technology on Tails to make him act like a traitor. Rouge, being the astute character she is, notices something is off. She has to fight against Tails while also trying to find a way to break the mind - control, leading to a complex and exciting story.
Perhaps Rouge is framed as a traitor by an old enemy. Tails initially doubts her but then realizes she's been set up. They then embark on a journey to find evidence to prove her innocence. Along the way, they face many challenges and their friendship is put to the test.
One plot idea could be that they have to keep their marriage a secret from their enemies at first. This would add an element of mystery and danger as they try to balance their normal heroic duties with their new relationship status.
Dr. Eggman could be a likely main antagonist. He might use his cunning and various inventions to manipulate the situation and make it seem like Tails or Rouge are traitors in order to further his own evil plans, like taking over the world or stealing some valuable chaos emeralds.
A great plot might involve the traitor's family. How do they react to the accusations? Do they believe in the traitor's innocence? For example, a sister could embark on a journey to find evidence to prove her sibling's loyalty. This would add a lot of emotional depth to the fanfiction.
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.
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.
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.
Perhaps Rouge is sent to the Naruto world to retrieve a powerful artifact that has been lost there. She enlists Naruto's help as he knows the land well. As they search for the artifact, they encounter many challenges like other ninja clans who also want the artifact. Naruto's ninja skills and Rouge's acrobatic and thieving abilities combine to make a great team.
One idea could be that Rouge discovers Danny's secret identity and tries to use it to her advantage in some way, like getting information from the Ghost Zone. Another could be a team - up where they have to face a common enemy that is causing chaos in both the human world and the world Rouge is familiar with.