The Clues to Inara's Illness - Firefly's best hidden subplot

The best hidden subplot in Firefly looks to be tackled soon in the new Novel, Life Signs, releasing in March 2021. I thought it would be interesting to collect all the clues from the series that point toward there being more to Inara than meets the eye. Morena's 'reveal' at DragonCon 2008:    • Morena Baccarin - Inara's Secret