Fossils can also be a theme in a more metaphorical sense. They can represent the past, and a story could be about how the past (symbolized by fossils) affects the present. In a family - drama - type of fiction book, an old family heirloom that is a fossil could be the source of family secrets and tensions.
Another way is through time - travel fiction. If a character travels back in time to the era when the fossils were formed, the reader gets to see the origin of the fossils. This can be used to teach about the history of life on Earth in an engaging fictional narrative. For example, a character might go back to the Jurassic period and witness the dinosaurs whose remains became fossils, and then come back to the present with new knowledge and a changed perspective.
Yes, they can. Fossils can be a central theme. For instance, a story could revolve around a character's obsession with finding a particular fossil. This could drive the plot forward as the character faces various obstacles in their search.