The rust plague was a virus that attacked the Daleks' casing, and in turn, killed the Dalek mutants inside.
It was created on Skaro when an accident at a weapons factory produced a radioactive cloud of metal-eating rust that destroyed a tracking station. The Daleks working there and a squad of Daleks on hoverbouts tried to destroy it. Their Brain Machine advised destroying the cloud by trapping it in a magnetic field and then spraying it with oil vapour.
This created a viral form of the cloud, which turned the Black Dalek Leader into a carrier of the plague. He unknowingly infected and destroyed all the Daleks who came into contact with him. When the Dalek Emperor returned from Solturis, he realised that the Black Dalek Leader was the carrier. Having also realised this, the Black Dalek Leader exposed himself to the plague as a form of atonement, only for the Emperor to deem him too valuable, ordering that the Black Dalek Leader's casing be reconstructed. (COMIC: Plague of Death)
The plague proved a sufficient enough distraction to the Daleks so as to allow the Monstrons to invade Skaro undetected. (COMIC: The Menace of the Monstrons)