Romana's rebels use the shattered remains of Gallifrey's great Academy as a base of operations in their war against Imperiatrix Pandora. But Pandora's anomalous existence within Romana's first incarnation is fracturing her mind. Only bonding with Romana's current form can stabilize her. The Imperiatrix discovers the newly acquired rebel headquarters and orders it destroyed, but their leader must be captured alive. Pandora's other advantage is the completion of a stronger strain of the Dogma Virus, infused with her own biology.
Meanwhile, Romana's plan is a showdown within the Matrix, one of the oldest repositories of information in the universe, containing the memories and knowledge of every Time Lord that has ever existed. She, Leela and K-9 trick Pandora into a dark partition, but the Matrix has become infected with the virus. Romana intends to sacrifice herself to end the conflict, but all three of them escape. With Pandora and her virus still trapped inside, the Matrix is destroyed forever.