Moriarty and the Apothecary
No, not in the same story. (Come to think of it, that's a story someone should write.) We just watched two anime series that were a world apart, yet shared intricate conspiracies and protagonists who notice what everyone else misses. And both had themes of low-born individuals standing against the abuses of the upper class.
Moriarty the Patriot casts Sherlock Holmes' arch nemesis as a fervent believer in dismantling the oppressive British class system. Using a number of stories from Sir Arthur Conan Doyle, the series bends the episodes into an overarching plot to bring about social reform without the devastating loss of life caused by the French Revolution. All the characters from the stories are here: Holmes, Mycroft, Lestrade, Irene Adler, Milverton, and more. Stories like A Study in Scarlet and The Sign of Four form parts of a new narrative that were allegedly a repressed story behind the scenes of Doyle's tales. I thought it was clever and entertaining.
In Apothecary Diaries, set in Imperial China, a young girl named Maomao is kidnapped and sold into slavery in the Rear Palace (women's quarters). Trained by her father as an apothecary, she quickly identifies the cause of several deaths among the Emperor's concubines and children. This brings her to the notice of Jinshi, head eunuch of the Rear Palace, who employs her as a food taster while secretly deploying her detective talents to unravel the plots and deceits rampant in the palace. The dynamic between Maomao and Jinshi is a large part of the fun of this series.
Both are tales involving the powers of observation and deduction, and using those powers to help those oppressed by noble rulers.