Put on trial by the Time Lords and in a state of shock from seeing Peri’s death, the Doctor is allowed access to the Matrix to prepare his defence. Inside the virtual world containing the sum knowledge and experience of the Time Lords the Doctor meets his ‘Helper’, a wheelchair-using young girl named Anosia. Exhausted from scanning through so many of his future adventures, the Doctor takes a tea break with Anosia; she in turn shows him an adventure that will help prove his innocence: an incident aboard the Starship Hyperion III. When the Doctor challenges her choice, Anosia explains that the Time Lords have already chosen this adventure as his evidence, and have made several incriminating edits, including the removal of the Doctor planting an herbarium with Vervoid seeds modified to assure a benign continuation of their species. Knowing this will ensure the Doctor is found guilty of genocide, Anosia promises to transfer the original recording into the trial. The Doctor returns to the courtroom, his time spent inside the Matrix wiped from his memory. Meanwhile, the Valeyard pays another visit to Anosia: after breaking his promise to free her from the Matrix, the villain stops the upload of the recording that will exonerate the Doctor
The Valeyard seems immune to the effects of the Matrix's mind wipe. He also knows how to manipulate data so external layers show no sign of disruption.
This story takes place after the Mindwarp section of the Sixth Doctor's trial and while he is in the Matrix viewing the evidence for his defence.
Perhaps coincidentally, the Sixth Doctor's segment of PROSE: The Eight Doctors takes place contemporaneously with this adventure and deals with his future self assisting in his defence. As with this story, the Sixth Doctor does not retain the memory of this; in that case, this was due to the meeting taking place within a stasis bubble, temporally isolating the encounter.
The Sixth Doctor is reminded of Charley Pollard despite not having yet travelled with her from his point of view. This could be explained as having seen her in the Matrix projections.