Maybe they get caught in a magical spell that makes them reveal their true feelings. This leads to a tender kiss as they both realize how much they care for each other. Rouge could be the first to initiate it, surprising Shadow with her boldness.
Another plot could be set in a more peaceful time. They are stargazing on a rooftop, and the beauty of the moment makes Rouge lean in and kiss Shadow. He is initially taken aback but then reciprocates, and it marks a new level in their relationship.
A really cool storyline is when they are sent on a mission to a parallel dimension. In this dimension, their personalities are slightly different, and they have to adapt while still trying to achieve their mission goals. It's interesting to see how they interact with the alternate versions of themselves and other characters. This type of fanfiction often explores the concept of identity and how their relationship might change in different circumstances. And it can be full of action, mystery, and character development.
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.
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.
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.
One plot idea could be that on Halloween, Rouge discovers an ancient artifact in a spooky, abandoned castle. She enlists Shadow and Knuckles to help her figure out what it is. As they explore the castle, they encounter various traps and spooky creatures. Along the way, they start to have some friendly competitions and arguments, but also grow closer as a team.
One idea could be a story where Knuckles and Rouge have to team up to protect a hidden ancient relic from a new villain in the Sonic universe. They start off distrusting each other as usual, but as they face challenges, they gradually learn to work together better.
You could also focus on a side character's perspective. For instance, a friend of the main characters who has always secretly liked one of them. This character could try to interfere with the relationship in 'it started with a kiss' in the fanfiction, creating a lot of drama and tension in the story.
One idea could be a forbidden love story where a human falls in love with a succubus. The succubus is initially only interested in his energy but gradually develops real feelings. Another could be a story set in a magical academy where a succubus uses her kiss to gain an advantage in a competition, but then finds herself falling for one of her rivals.
One idea could be exploring a different backstory for the main characters. For example, what if the characters met in a completely different setting before the events of the original story? Another could be a 'what if' scenario where a character makes a different choice at a crucial moment in the story. Maybe a character decides to trust someone they originally didn't, which could lead to a whole new set of relationships and plot developments.