One common theme could be the exploration of their relationship in a more romantic and often homoerotic way. For example, there might be stories about their unspoken feelings for each other.
One possible fanfic could be about how Simon's glasses are not just a simple accessory but a symbol of his intelligence. Maybe in the fanfic, the glasses get lost and the other chipmunks go on a wild adventure to find them, realizing how important they are to Simon.
In Alvin x Simon fanfiction, they might go on an adventure together. For example, they could get lost in the forest while trying to find a special type of nut for a recipe. During their time lost, they rely on each other's skills. Alvin uses his quick thinking and physical abilities to get them out of some tricky situations, like crossing a small stream. Simon, on the other hand, uses his knowledge of the forest's flora and fauna to find food and shelter. Through this adventure, their bond grows stronger.
Well, aside from Simon, Alvin is bound to be a central figure. He'd probably come up with all sorts of crazy plans to get Simon well again. Theodore too, as he's always been close to Simon. He might be the one to notice the small changes in Simon's condition first. And of course, Dave could also be an important character. He's like their guardian, so he'd be involved in taking care of Simon, getting him to the vet if needed, and making sure the other chipmunks don't get into too much trouble while trying to help.
Fanfiction.net is also a good place to look. There are many users who contribute different types of fanfics, including those about Alvin and Simon. Just use the search function and type in 'alvin x simon' to see what pops up.
One great 'alvin x simon fanfic' story could be the one where they go on an adventure together in a magical forest. They face challenges and have to rely on each other, which deepens their bond.
Simon's calmness is also a good trait. In a fanfic, when Alvin and Theodore are panicking, Simon can stay calm and come up with a plan. Like if they're lost in the woods, Simon can analyze the situation, look at the stars or the plants around them to find their way home. He is also very observant, which means he can notice small details that others miss. This can lead to interesting plot twists, such as when he notices a strange mark on a tree that leads them to a hidden treasure.
One idea could be Simon getting lost in a magical library and having to use his intelligence to find his way out while also uncovering secrets about the Chipmunks' past. Another could be Simon falling in love with a new character who challenges his intellectual side and makes him see things in a different way. Or perhaps Simon having to save the day when Alvin and Theodore get into a really big mess by using his scientific knowledge.
In this fanfic, Simon could get sick from an encounter with a new, unknown substance in their environment. This makes him act in very un - Simon - like ways. Alvin and Theodore are initially confused but then realize they need to find a cure. They might go on an adventure to seek help from other animal friends or even humans who are kind to them. Along the way, they face various challenges and obstacles that test their determination to save Simon. This fanfic could also explore the emotional side of the chipmunks as they worry about losing Simon.