Dr Godalming had her mind and identity altered by Heights Pharmaceuticals to achieve their goals, making her believe that "Luke Palmer" was her husband to motivate her during the Invictus breakout. She could not remember her real name. (AUDIO: "Invasion: Kill")
Working for a minister and the Ministry of Health, Dr Godalming gave Luke a gun at the police station to encourage the spread of the virus. She initiated the quarantine of Cardiff and shot Andy Davidson when he subdued Luke. (AUDIO: "Incubation: Know") She announced on the news that a vaccine would soon be available.
When Jack Harkness's personal data was uploaded to the Data Core, (AUDIO: "Prodromal: Love") Dr Godalming informed the minister and had her men collect Jack's body, believing that he had wiped out Torchwood. She began the "inoculation" with Provictus, having those infected with the 1950s strain killed or left to die. The minister later told her that she was to administer the virus to the whole of the UK.
Jack told Dr Godalming that he had deactivated all strains of the virus using a trojan horse in his personal data and made her realise that she and Luke had been used. She drove away from the city, wishing them all dead, when she realised that Luke was in the backseat. He told her to keep driving and that they would see what happened. (AUDIO: "Invasion: Kill")
Dr Godalming was motivated by self-preservation, wanting to save herself from being killed by Luke. She admitted to Jack that she felt bad about bringing about the end of free thought in Cardiff but wished death upon all its citizens when she failed in her mission and was forced to flee. (AUDIO: "Invasion: Kill")