Sure. There are some great ones out there. You might try searching for tags related to 'tfp megatron x starscream' on different fanfic platforms. The quality can vary, but you're likely to come across stories that really delve into their characters and the unique relationship they have in the Transformers: Prime universe.
There's also the theme of redemption. Sometimes, in these fanfictions, their relationship is a part of a larger story where they both try to find redemption from their Decepticon ways. They might see each other as a way out of the cycle of violence and destruction that the Decepticons are involved in, and their relationship becomes a catalyst for their character development.
I really like 'The Unspoken Bond'. In this fanfic, Starscream and Soundwave's relationship is explored in a more psychological way. It shows how they understand each other on a level that others in the Decepticon faction don't. The writing is quite engaging, with a lot of descriptive passages that bring the Transformers' world to life. It also has some really interesting plot twists that keep you hooked from start to finish.
Archive of Our Own (AO3) is a great place to start. It has a large collection of Transformers fanfics, and you can easily search for the specific pairing of Megatron and Starscream from TFP. Just use the search bar and type in relevant tags.
There are also fanfictions that explore a more complex relationship between them. Maybe there are hidden feelings or a deeper understanding that they have for each other despite their differences. This can lead to stories that are more about emotional exploration and character development rather than just action and power struggles.
Archive of Our Own (AO3) is a great place to start. It has a large collection of Transformers fanfics, including many focused on the Starscream x Soundwave pairing in the Tfp universe. The site has a good search function that allows you to filter by tags, so you can easily find what you're looking for.
One plot idea could be that Starscream and Arcee are forced to team up during a crisis on Cybertron. Maybe a new threat emerges that endangers both Autobots and Decepticons, and they find that they have to rely on each other's skills. For example, Starscream's flight abilities combined with Arcee's combat skills could be a great asset. Another idea is that there is some sort of memory - sharing accident. Starscream and Arcee end up seeing each other's pasts and gain a new understanding of one another, leading to a strange, new relationship.
Another place to look could be FanFiction.net. Although the interface might not be as modern as AO3, it still has a vast collection of fanfictions. Some of the older and more popular tfp knockout x starscream fanfictions might be there. You may need to dig a bit deeper by exploring different categories related to Transformers Prime.
One way their relationship could develop uniquely is through a shared interest in ancient Cybertronian technology. Suppose they both stumble upon an old relic that holds great power. They have to collaborate to understand and control it. In the process, they start to respect each other's intelligence and skills, which gradually turns into a deeper connection. Also, if they were to be stranded together on a desolate planet for a while, they would be forced to rely on each other, and this could lead to a very different kind of relationship compared to their usual Autobot - Decepticon dynamic.
Fanfiction.net is also a great place to look. There are numerous writers who create stories about different Transformers pairings. However, the quality may vary, so you might need to read through a few to find the really good ones about Megatron and Starscream.