Maybe a fanfiction where Knuckles has to protect Tails during a dangerous situation, like an invasion by a new enemy. This could show their friendship and how they rely on each other's strengths.
You could also write a fanfiction that focuses on Knuckles' relationships. For example, how he becomes friends with a new character introduced by the Game Grumps. Show his growth as a character as he learns to trust and rely on this new friend.
One idea could be a cake fanfic where the cakes come to life and have their own little society in a bakery. They could have different personalities based on their flavors, like a feisty chocolate cake and a sweet vanilla cake.
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.
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 Fionna and Cake find a magical portal that leads them to a parallel universe where all the characters have swapped genders. It would be a really fun and unique take on the Adventure Time world. Another idea is that they go on a quest to find the rarest ingredient for a cake that has the power to grant wishes. They could face many challenges along the way, like battling new and strange monsters.
A plot could revolve around Cake finding a long - lost relative. This relative could be a powerful and mysterious cat - like being who has some dark secrets. Fionna and Cake then have to decide whether to trust this newfound relative or not. Maybe this relative is being hunted by an even greater evil, and by helping, they put themselves in danger. It could also be a story where Fionna loses her memory and Cake has to take on the role of guiding her through their known world while also trying to find a way to restore her friend's memory.
Well, they could go on a quest to find a rare ingredient for a special cake that Jake wants to make. Along the way, they encounter various obstacles like a swamp full of gooey monsters or a forest with trees that can move. Also, a plot could be centered around Jake losing his stretching ability and Cake having to find a way to get it back for him. This would involve them visiting different parts of Ooo and asking for help from their friends.
I don't know the specific story Knuckles tells without more context. It could be an adventure story, a legend from his world, or something personal to him.