One popular 'Jackson Jekyll x Holt Hyde' fanfiction might be the one where they team up to solve a mystery in their school. It shows their unique dynamic, with Jackson's more reserved nature and Holt's wild side working together.
You can try fanfiction.net. It has a large collection of various fanfictions, and there's a good chance you'll find some great 'Jackson Jekyll x Holt Hyde' stories there.
One idea could be that Jackson and Holt have to work together to solve a mystery in their school that involves a strange new student who seems to have powers related to their own. Another could be a story where they get swapped at an inopportune time, like during a big school presentation, and have to figure out how to get back to normal without causing too much chaos.
How about Spectra Vondergeist? She could add an element of mystery to the fanfiction. She might be spying on Jackson and Holt for some unknown reason, which could create a lot of suspense. Additionally, Operetta could be in the story. She could provide some musical relief or even use her music - related powers to help Jackson and Holt in a tight situation, like calming them down when their Jekyll and Hyde transformation is getting out of control.
Secrecy is another theme. Jekyll's secret about his transformation into Hyde is a central part of the story. In the fanfiction, Utterson's attempts to either uncover or protect that secret are often explored. How he deals with the knowledge that his friend is hiding something so huge is a major part of the narrative in many of these fanfictions. This can lead to a lot of tension and drama in the relationship between Utterson and Jekyll.
Basically, the tale of Jekyll and Hyde centers on Dr. Jekyll's experiments with a concoction that leads to his transformation into the evil Mr. Hyde. It delves into the darker side of human personality and the consequences of unleashing it.
In Jekyll and Hyde fanfiction with time travel, it could be about Hyde traveling back to prevent his own creation. Maybe he realizes the chaos he has caused and wants to change the past. This would add a whole new layer of complexity to the story, as he has to deal with his own duality in a different time period.