The Valeyard appears in all four segments of the 1986 serial The Trial of a Time Lord – The Mysterious Planet, Mindwarp, Terror of the Vervoids and The Ultimate Foe.

As prosecutor, the Valeyard presented the events of The Mysterious Planet and Mindwarp as extracts from the Matrix, the computer network that serves as the repository of all Time Lord knowledge.

Throughout the presentation of the evidence the Doctor barked at the Valeyard, calling him names such as "the Boneyard," "the Scrapyard," and "the Knacker's Yard," and only the interventions of the Inquisitor, another Time Lord, kept the trial going.

Scenes of the mercenary Sabalom Glitz attempting to buy "secrets" from the robot Drathro were censored completely.

In the Matrix extract, it appeared that Yrcanos was maneuvered into killing the Mentors after Kiv's mind had been transplanted into the body of the Doctor's companion Peri – the Doctor having apparently abandoned Peri to save himself after exposure to one of the machines in the lab temporarily altered his personality – effectively killing her.

The Doctor was shown being forced to destroy the human-plant hybrids known as the Vervoids when they ran rampant on a space liner.

Sabalom Glitz and the Doctor's future companion Melanie Bush were presented to the Court to rebut the Valeyard's accusations.

This concept is similar to the ethereal "Watcher" that manifested itself to bridge the gap between the Doctor's fourth and fifth incarnations (Logopolis).

The Valeyard was also revealed to be acting at the behest of the High Council of Time Lords to cover its corruption in the Ravalox affair.

Ravalox was Earth in approximately 2,000,000 AD, but the Time Lords moved it through space, killing virtually every human being living on it.

The Master reinforces the statement made in The Ultimate Foe to the Eighth Doctor—that the Valeyard is "an amalgam of the Doctor's darker side, somewhere between his twelfth and thirteenth regenerations."

After possessing the body of the Keeper, he acquires control over the Dark Matrix, the repository of all of the Time Lords' most evil impulses, and tries to use it to take revenge on the Doctor.

However, the Seventh Doctor escapes the Valeyard's attack by sealing his conscious mind away from the assault in the TARDIS telepathic circuits, although this briefly leaves him as nothing more than an amnesic cardsharp who calls himself "Johnny".

Having regained his memory after retrieving the circuits, the Doctor confronts the Valeyard (now calling himself "the Ripper" on the grounds that the name is more evocative) in a church where the Ripper has left his TARDIS, now reprogrammed into the appearance of the Doctor's tomb, causing his foe to lose control of the Dark Matrix, provoking it by revealing that the Dark Matrix is just as trapped under the Valeyard's control as it was on Gallifrey.

Connecting plot lines from the Virgin novels' New and Missing Adventures range, the narrative centred upon the circumstances involving the sixth Doctor's regeneration and also the purpose and origins of the Valeyard.

The Valeyard claims he was created on a planet orbiting Eta Rho by the Thirteenth Doctor, who was experimenting with ways to break the regeneration limit.

Although the Valeyard's plan succeeds in allowing him to essentially 'transplant' himself over the Doctor's timeline with the goal that he will then spread throughout the Matrix and replace all other Time Lords, the remnants of the Doctor's psyche in the Matrix after his 'death' are able to undo the Valeyard's attack by reaching back into his past and prompting his past self to set a course that will expose the TARDIS to a dangerous form of radiation, causing the Sixth Doctor to regenerate and thus purging his body of the Valeyard's influence, leaving his foe trapped in the Matrix as his victory is erased (The Brink of Death).