At some point, the Eleven regenerated 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)