The Doctor continues his quest to capture and stop the Valeyard, the Master assists him with the help of Glitz, leaving everyone to wonder if the Master may have plans of his own for the Doctor and the Time Lords. As things progress, in the strange world of the Valeyard the Doctor comes closer to either stopping the Valeyards evil plans or the end of his existence.

As the trial of the Doctor continues, an old foe of the Doctor makes an appearance startling the Doctor, the keeper of the Matrix and the Inquisitor alike. The Doctor and the court then discovers who the Valeyard really is. The Doctor goes inside the Matrix after the Valeyard in an attempt to capture him and also prove his innocence in the process.

The Vervoids overhear what is planned for them and begin their attempt to prevent it from happening. The ship starts to head towards a black hole and in the attempt to save it, the ship ends up being hijacked adding to the already existing problems. The Doctor then assists the crew in saving their ship and in the process ends up being charged with a more serious charge in the Time Lords trial.

Mel overhears someone plotting to kill all the animal-king onboard the Hyperion and has taped the conversation, unfortunately the tape vanishes. Meanwhile Bruchner is becoming increasingly worried about the situation in the Hydrophics Centre. It is soon discovered that the creatures that emerged from the pods are Vervoids and they are using the ships air ducts to move around unseen.

The crew of the Hyperion discover that the Pods have been opened, The Doctor is brought to the bridge where Commander Travers questions him and Mel about murders and disappearing bodies. The Doctor starts to wonder about Dr. Laskey and decides to investigate her.

Arriving back in the courtroom, the Doctor starts his defense by showing the future beginning with his arrival onboard the spaceship Hyperion III which is on it's way from the planet Mogar to Earth with a cargo of rare metals. The Doctor shows the court that the TARDIS picked up a distress signal and he responded to it. Upon arrival, the Doctor tells Mel that he can sense evil. They are then captured and brought before Commodore Travers.

The Doctor works to free king Yrcanos and Dorf. Kiv prepares for his surgical procedure and Peri is strapped down and shaved in preparation, before the Doctor can help her, the Time Lords extract him for the Trial. The Valeyard then presents what happened next from The Matrix files and the Doctor is shocked at what he see's occur.

Dr. Crozier prepares to transplant Mentor's brain with the help of the Doctor, while king Yrcanos, Peri and Dorf prepare to attack the Mentors. In the laboratory, Dr. Crozier decides that Peri may be a compatible body donor and sends for her.

As the Valeyard presents events to the Doctor and the Time Lords, the Doctor informs them that he does not remember the events occurring. Peri encounters Matrona who allows her to join Mentor's servants in order to protect her from the guard. As things progress, the Doctor's behavior becomes more erratic as he trys to mislead Dr. Crozier.

After arguments, the Inquisitor warns both the Doctor and the Valeyard, reminding them that they are in judicial proceedings and to behave. The Valeyard then presents evidence relating to the Doctor landing his TARDIS on the planet Thoros Beta where the Doctor and Peri flee in order to avoid being accused of a crime they did not commit. In the process they arrive at a experimental laboratory where they rescue King Yrcanos.

Queen Katryca and the rest of the tribesmen arrive at the underground bunker where they confront Drathro The Immortal one. The Doctor tries to convince Drathro that he will repair the Black Light system while he fears that a possible upcoming explosion of the system could have the potential to destroy the universe.

The Doctor escapes from the Immortal one and goes to the local tribe, there he is imprisoned along with Glitz and the Immortal one sends a service robot out to retrieve the escaped Time Lord. While the Doctor is imprisoned with Glitz awaiting execution, Glitz informs the Doctor of the true name of the planet.

The Doctor is saved from the stoning in the nick of time and taken to see the Immortal who wants to use the Doctors far greater knowledge to his advantage. Meanwhile, Peri is taken before Queen Katryca of the local tribe and told that she is to become part of the tribe and take many husbands because there is a shortage of women.

The Doctor is taken to a Time Lord space Station and put on trial for his life. The Valeyard uses past examples of the Doctors activities taken from 'The Matrix', the repository of all Gallifreyan knowledge to show how the Doctor has interfered with other worlds. In this installment of the Trial story Arc, The Doctor's visit to the planet Ravalox is told and how he interfered with the indigenous population of that world when he saved it from a devastating explosion.