Inara was dying, which is why when Simon says ‘I don’t want to die on this ship’ she replies with ‘I don’t want to die at all.’ Simon tried to cure her and fail.
Future episode: Flashback to Inara and Malcolm before the time the show took place. Inara took an anti-rape drug that would kill anyone who raped her, and was taken by reavers. When malcolm finds her, he finds her in a room full of dead reavers (meaning they all did), takes her hand, and treats her like a lady for the first time.
Serenity goes to a winter-y planet, the crew is taken in by very friendly people. The crew later catches the inhabitants trying to steal Serenity, and the inhabitants reveal that they’re planet is dying and they need to escape. There isn’t enough air or food on the ship to take everyone (both crew + planet inhabitants), unless somehow they get lucky and another ship finds them after Serenity take off. Malcolm tells everyone to sleep on it and they’d decide in the morning. Then, he locks himself on the bridge and takes off in the middle of the night while the crew is sleeping on the ship and inhabitants sleeping in their homes, leaving the inhabitants to die. They never pass any other ships in their escape from the planet, meaning if they had rescued the inhabitants, everyone would have died.
Based on these episode ideas, Joss and the writers would have truly taken this show to another level with gritty, intense drama that was barely touched upon in the episodes released.