“A Clockwork Nebari” is episode eighteen of season two of Farscape.
Chiana has been getting information on D’Argo’s son, using methods that Crichton doesn’t approve of. Rygel and Aeryn return separately, and they’re behaving oddly. That’s because they’ve had their minds tampered with by a Nebari – and they want Chiana. The crew is captured, including Pilot, and mind cleansed. The Nebari are injured after an encounter with a Peacekeeper ship.
Chiana and her brother, and many more, had been infected with a disease, known as the Contagion (a disease basically called ‘disease’? Well, I suppose Earth has one called ‘Plague’), by the Establishment, and sent out to spread it. There are flashbacks of Chiana and her brother.
It turns out that Chiana’s brother isn’t dead, as she had thought in “Taking the Stone”.