One night in December, during the blackout, she was attacked by a RATS, which believed her to be carrying a Gallifreyan artefact known as an Augur's Stone. The Ninth Doctor saved her but the RATS continued to pursue her. When she encountered the Doctor and the RATS again, Hetty learned they were after the Stone, which was being held at Admiralty House. Hetty fled to warn Churchill and the other members of the Admiralty before the RATS invaded.
During the RATS raid, Hetty absorbed the knowledge of the Stone. Through this, she learned that the RATS were seeking to augment their own artificial intelligence by obtaining it, while the Doctor sought to save them by preventing this, as he knew they would be unable to handle the power and overload. Hetty then lost consciousness and the RATS grabbed the Stone, destroying themselves. Afterwards, the Doctor helped Hetty regain consciousness (AUDIO: The Oncoming Storm)
In Autumn 1941, Churchill encountered the Black Dog at his home in Chartwell, but the Security Services did not believe the story and questioned the then-Prime Minister's sanity. Hetty believed the incident really happened and feared for Churchill's safety. She tried to contact the Doctor via a letter out of desperation. She met the Tenth Doctor in Piccadilly, whom she believed to be a British intelligence officer named John Smith, to discuss Churchill's experience. This was a betrayal of confidence and Major Wheatley arrived to arrest the Doctor as a Nazi spy. Hetty then met Churchill at Admiralty House to explain herself. She convinced Churchill of her intentions but he still felt it necessary to sack her as his secretary and find her some alternative employment.
Leaving Admiralty House, Hetty infiltrated the prison in which the Doctor was being held and freed him. When they returned to assist Churchill, a Swami Kahn Tareen under Wheatley's orders released the Black Dog, an entity which travelled through a host, and passed it off as belonging to Churchill. The group chased the hound through London. After a number of deaths, the Doctor realised that only a more powerful "Black Dog", a manifestation of someone's darkest emotions, could stop the hound. Hetty sacrificed herself to the hound in the hopes of sparking these emotions among Churchill. After Hetty was killed, a manifestation of the Doctor's inner demons vanquished the hound.
Hetty's body was buried by her family back home in northern England. Officially, she was another casualty of the Blitz. She was remembered as the girl who stood up to Churchill, which not even Adolf Hitler had managed to do. (AUDIO: Hounded)