One great place to start looking for Firefly Mal and Inara fanfiction is Archive of Our Own (AO3). There are numerous stories there that explore their relationship in various ways. Some might focus on their unspoken feelings during the events of the show, while others could be AU (alternate universe) stories that place them in different settings like a modern-day Earth or a fantasy realm.
There are also some fanfiction stories that explore what could have happened after the events of the series. In one of them, Mal and Inara finally admitted their love for each other and decided to start a new life away from the Serenity. It was really heart - warming to read how they overcame all the obstacles that were in their way, both from their own personalities and from the external circumstances of their world.