One main theme is loyalty. Given their characters, the exploration of whether they are truly loyal to each other or have their own hidden agendas is often a key part. For example, in many fanfics, Kisaki's manipulative nature might put their loyalty to the test.
There's also 'The Unlikely Alliance'. In this fanfic, Kisaki and Hanma find themselves in a situation where they have to work together against a common enemy. It shows a different side of their relationship, with some interesting plot twists.