After attempting to make a deal with the Master, the Eleven was shot by the "Deathworm" Master, the "War" Master and Missy, and regenerated (AUDIO: Day of the Master) into a female body. The Twelve had a much better control of the incarnations within her mind, due to a neural inhibitor given to her by the Time Lords, although she also considered herself as possessing the firm hand necessary to keep them all in line even without the chip. She was assigned on a mission by the High Council to help the Eighth Doctor investigate the origins of an Ogron which declared itself to also be the Doctor.
She was captured by the Daleks, along with the Doctor and Bliss and taken to a facility with her memory suppressed. She was given the name "Pi Gamma" by Bliss. Without her neural inhibitor, she had to work harder to keep her other incarnations suppressed. She attempted to break out of the facility, with her previous incarnations prodding and goading her, forcing her to develop a means of disrupting the transmat technology using the cybernetic components of another prisoner. (AUDIO: In the Garden of Death)
After the encounter with the Daleks on Uzmal, when the Time Lords investigated a creature that was meant to be living there based on the Twelve's memories, Cardinal Ollistra had the Twelve put into stasis. (AUDIO: Jonah)
Shortly after being put into stasis, the Twelve convinced a dreadshade to release her; the Dreadshade was the only living being in the armoury not kept in stasis as its own terror would normally keep it contained, but after the Valeyard's actions had erased the Daleks from existence the Dreadshade had lost its immobilising terror of the Daleks. The Twelve tried to use the Dreadshade to blackmail the Time Lords into giving her a seat on the High Council, but when she mentioned the Daleks (which she still remembered as she had been in stasis when they were erased), it sparked a new wave of terror from the Dreadshade that caused it to explode. The Twelve was lost in the subsequent explosion. (AUDIO: Dreadshade)
When Liv Chenka was trying to work out the identity of the "War" Master, she initially thought he might have been this Renegade, also speculating that he might have been the Thirteen. (AUDIO: Day of the Master)