The story made up of episodes 5-8 is generally referred to as Mindwarp.

The Valeyard's evidence against the Doctor continues with an account of his adventure on the planet Thoros-Beta in the 24th century, last quarter, fourth year, seventh month, third day. 

The Doctor and Peri arrive on a coastal beach on Thoros-Beta, the Doctor having decided to investigate after learning from the dying words of a Warlord of Thordon that phasers - technologically advanced and highly dangerous weapons - are being supplied from this planet. Exploring a tidal cave, the travellers are attacked by a squid-like creature, the Raak, which has apparently been stationed there to operate machinery extracting energy from the sea water. The Doctor kills the Raak with the phaser which he acquired from the dying Warlord. 

This act is cited as proof by the Valeyard of the Doctor's inherently violent nature. The Doctor protests that the death was an accident. 

The Doctor and Peri are captured by humanoid guards and taken to the laboratory of a scientist named Crozier, whom the guard leader had assumed they were here to see. They escape before the mistake is discovered and, in some nearby tunnels, find a wolf-creature, the Lukoser (Thomas Branch), chained to the wall. A procession of Mentors, natives of Thoros-Beta, then passes by, and amongst their number is Sil (Nabil Shaban). 

Crozier (Patrick Ryecart) has been conducting experiments in brain transference, his ultimate aim being to transfer the brain of the Mentor leader, Kiv (Christopher Ryan), into a new body, it having outgrown its own. He has also been using a cell discriminator device to pacify the belligerent King Yrcanos (Brian Blessed), a Krontep warrior, who is currently lying on a bed in the laboratory. 

The Doctor and Peri make their way back to the laboratory. The Doctor starts to disconnect the circuitry but is discovered by Sil, who decides to use the cell discriminator on him. The process has already been started when Yrcanos suddenly revives and starts smashing up the laboratory. Eventually the warrior escapes into the tunnels. 

The Doctor's mind has apparently been affected by the process he has undergone, and he becomes callous and self-interested. He offers to help Crozier repair the lab and assists Sil with some interplanetary currency speculation before betraying Peri to the Mentors. His bewildered companion is chained to the Rock of Sorrows on the jagged coastline outside the city and the Doctor tries to get her to confess to being a spy from Thoros-Alpha. 

The Doctor objects. He cannot clearly remember the events, but is sure that the evidence being presented has been falsified. The Valeyard states that it is impossible to tamper with the Matrix. 

While escorting Peri back into the base for further questioning, the Doctor is ambushed by Yrcanos and flees. Peri then accompanies Yrcanos - who wishes her to become his bride - as he resolves to locate an Alphan resistance movement which he assumes is present on the planet. The Lukoser turns out to be Yrcanos's loyal equerry, Dorf, who has fallen victim to Crozier's experiments. 

Crozier has meanwhile found a temporary body in which to house Kiv's brain. It is that of a Mentor fisherman found floating dead in the sea. The transfer is achieved successfully after several nerve-wracking false alarms - Kiv had ordered that both Crozier and Sil be killed if the operation failed. 

Yrcanos finds the Alphan resistance group and Peri manages to win over their leader, Tuza (Gordon Warnecke). They all head for Alphans' weapons dump but are ambushed by the Mentors' guards and knocked unconscious. 

As neither the Doctor nor the Alphans are suitable candidates for the transference of Kiv's brain, Crozier must find another host. He wonders if Peri would be suitable. The Doctor, now acting more like his true self, goes to the Induction centre - the area where new Thoros-Alphan prisoners are taken for conditioning with brain implants - to see if he can find anyone else. He frees Tuza, rescues Yrcanos and Dorf from a cell, and then heads off to save Peri, who is being prepared to become the ultimate recipient of Lord Kiv's intelligence. Dorf is killed by guards and, in a rage, Yrcanos destroys the control centre. The Alphan slaves mill about in confusion as their brain implants are no longer operative. 

Before he can rescue Peri, the Doctor is taken out of time by the Time Lords and transported to their space station to begin his trial. The transference operation is completed successfully by Crozier, and Kiv awakes in the body of Peri, whose own mind ceases to exist. Yrcanos, along with Tuza, has been temporarily frozen in time by the Time Lords, but he is released at this point and forces his way into the laboratory. Unable to stand the sight of his intended bride possessed by Kiv's consciousness, he fires a phaser indiscriminately about the room, destroying everything within - the result which the Time Lords had intended to achieve, to eliminate the threat which they considered the transference equipment to pose to the natural course of evolution. 

The Doctor is aghast at what he has seen and angrily disputes the Inquisitor's claim that the High Council had no choice but to intervene. He asserts that there is more to the Trial than has so far been revealed, and that he intends to discover what it is.

Synopsis from Doctor Who: The Sixth Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos