The TARDIS is drawn to a space station where the Doctor is subjected to a Time Lord inquiry into his behaviour, presided over by an Inquisitor. The prosecuting counsel, the Valeyard, presents the first piece of his evidence, which consists of a recording played back on a screen linked to the Matrix. It concerns a visit by the Doctor and Peri to the desolate planet Ravolox, which turns out to be a future Earth, shifted light-years through space.

The court watches as the pair get caught up in a conflict between the surface-dwelling Tribe of the Free, led by Queen Katryca, and the planet's other inhabitants, a group of subterranean technocrats and their robotic ruler Drathro.

Two shady off-worlders, Glitz and Dibber, are meanwhile attempting to appropriate from Drathro some mysterious 'secrets' - details of which are censored from the Matrix record. The 'secrets' are eventually destroyed, along with Drathro, as a result of the Doctor's actions.

The Valeyard's second segment of evidence relates to the planet Thoros-Beta. Here the Doctor and Peri meet their old adversary Sil and others of his Mentor race, whose leader Kiv is awaiting an operation from a scientist named Crozier to transplant his brain into another body. They also form an uneasy alliance with a kidnapped Krontep warrior, King Yrcanos, and encounter a group of resistance fighters. Peri is eventually chosen as the recipient of Kiv's consciousness and is apparently killed in an ensuing mêlée sanctioned by the Time Lords to prevent Crozier's work from disturbing the balance of nature.

The distraught Doctor gives the court his evidence for the defence. He chooses an incident from his own future, in which he and his companion Mel arrive on the space liner Hyperion III in response to a distress call. There they battle against and ultimately destroy a hostile race of alien plants, the Vervoids, while also helping to thwart a mutiny by the ship's security officer, Rudge.

With the evidence complete, the Doctor learns that the Master has gained illicit access to the Matrix in his TARDIS. Glitz is now revealed to be the Master's associate and the 'secrets' to be information stolen from the Matrix.

The Valeyard admits his identity as a distillation of the dark side of the Doctor's nature, somewhere between his twelfth and thirteenth incarnations, out to take control over his remaining lives.

With the help of Mel, who along with Glitz has been brought to the space station by the Master, the Doctor defeats his future self - although, as they leave in the TARDIS with all charges in the trial having been dropped, it appears that the Valeyard has taken over the body of the Keeper of the Matrix and may not have been as completely vanquished as they had thought...