Three months after the Doctor's arrival, and the day after Atrias' birthday party, the neighbouring planet Baralda was attacked by the Daleks using the Time Destructor. After receiving a distress call from First Citizen Togrok, Atrias suffered a nervous breakdown after the Dalek Supreme demanded he surrender and hand over the population to become Dalek slaves, or they would suffer the fate of Baralda. Atrias accepted the terms and fled the Council Chamber. The Doctor and Captain Parlos were disgusted by his display of cowardice and effectively took charge in his place as the Harvest of Urbinia began.
Atrias attempted to leave the planet in his own ship but it had been stolen during the chaotic evacuation. He was captured by the Daleks and brought before the Dalek Supreme, who ordered Atrias to enforce the surrender. Atrias claimed he was no longer in charge and it was the Doctor the Daleks wanted. The Dalek Supreme sent several Daleks to capture the Doctor and then exterminated Atrias.
At the end of the invasion, the Second Doctor averted the change in the timeline by ensuring the First Doctor arrived on Kembel to prevent the Time Destructor's completion. (AUDIO: Daughter of the Gods)