Ruta graveolens, or Rue as it’s commonly called has been used for medicine and magic for millennia. But one use not commonly known about is its use in fighting Bubonic plague.
Rue’s naturally pungent scent drives away bug, flies and in particular fleas, all of which helped fuel the spread of the plague. Its efficacy was an essential ingredient in the Four Thieves Vinegar, noted by M. Grieve’s in his work A Modern Herbal, which was used by grave robbers who plundered plague victims’ graves.
As for the source of the use of the word to denote negativity, such as “you’ll rue the day,” it’s believed that refers to the irritation caused by too much contact with Rue on the skin.