When Torchwood Three was rebuilt in Cardiff by Gwen Cooper, and everything started to go out of hand after the Sorvix took over the city administration, she revealed herself to Torchwood, penetrating the Hub (AUDIO: The Empty Hand), and announced that she will depose Jack Harkness and become the new leader of Torchwood.
Under her leadership, Torchwood stopped psychic attacks on people through the words "I know what you've done. I know what you'll do." The words targeted people's guilt for the most horrible actions in their lives, encouraging them to do more. But when they attacked Yvonne, she didn't show any guilt at all, believing that all her terrible actions were necessary. She did, however, felt sorry for Orr, after putting them through a painful experience in order to track down the words' origin. (AUDIO: Tagged)
After she sent Gwen and Mr Colchester to investigate an escape room, which nearly killed them (AUDIO: Escape Room), Yvonne arranged a deal between Ro-Jedda, the leader of the Sorvix, and Prime Minister Felicity in order to improve the United Kingdom's economy. Yvonne then brought down the Red Doors movement and survived the explosion with Ro-Jedda, only to witness that the Sorvix' god come through the Rift. (AUDIO: Herald of the Dawn)