Removed from time, the Doctor stumbles out of the TARDIS to find himself in a chamber within some mysterious space station. Going through a set of doors nearby, the Doctor finds himself facing a group of Time Lords. Among them, The Valeyard - a prosecuting counsel. An Inquisitor arrives - the court is in session. Amazed, the Doctor realises that he is being put on trial. The Valeyard asks the court to watch the viewer and observe an incident from the past when the Doctor and his then travelling companion, Peri, arrive on the planet of Ravalox. An Earth-like planet that appears to be recovering rapidly from a devastating encounter with a solar fireball, Ravalox is a planet wrapped in mystery. Records are hazy about it and with its amazing recovery from the fireball, the Doctor is tempted to write a thesis on the planet. However, when the two travellers stumble across access to an underground chamber they find themselves...in Marble Arch Station. Despite its location in a different part of the galaxy and the records identifying it as Ravalox...the planet appears to be Earth!

Two men have been watching the Doctor and Peri. Concerned that they may gain access to the underground city, Glitz and Dibber make contact with the tribe that lives on the surface. An attempt to convince the tribe that their Great Totem is a navigation hazard fails and Glitz and Dibber are taken prisoner. They are soon joined by Peri who had earlier chosen not to venture any further underground with the Doctor. In the meantime, the Doctor has found his way into the underground city where he finds that water is a precious resource, its theft punishable by death, at the command of the Immortal...

For his second item of evidence in the prosecution of the Doctor, the Valeyard requests that the court watch the viewscreen and observe the events that transpired just before the Doctor was removed from time.

The Doctor and Peri arrive on Thoros Beta, intrigued by a dying warrior's request for more "beams that kill". An encounter with a sea creature operating a defence barrier nearly proves fatal and when it is killed, by accident, an investigation is launched. Eluding the investigators, the Doctor and Peri have a narrow encounter with a wolfman chained up in one of the tunnels. As they try to find their way out, they catch sight of a familiar face - Sil. Peri is horrified to discover that Thoros Beta is Sil's home planet and her desire to get away is stronger than ever. Despite this, the Doctor insists on investigating further and in a nearby lab they find King Yrcanos strapped down on an operating table, a device attached to his head, interfering with his brain waves. The Doctor's attempt to dismantle the device is thwarted when Sil and others return. Strapped into the device the Doctor is subjected to something which appears to alter his brain waves...for shortly afterwards he betrays Peri and Yrcanos to Sio and the guards.

Peri and Yrcanos make their escape and encounter the wolfman, who turns out to be the latter's equerry, modified by Crozier's experiments. Yrcanos vows to kill the Doctor but he intends to overthrow first the Mentors led by Lord Kiv. In the meantime, the Doctor appears to have allied himself with the Mentors. Has Crozier's device affected his thoughts or has the Doctor turned traitor to save his own skin...?

Presented with the chance to defend himself, the Doctor has looked into his future and found a series of events which he believes will show that he improves and that his conduct will be better fitting a Time Lord. As the court watches the viewscreen events begin to unfold on board the space cruiser Hyperion 3. En route to Earth it is carrying passengers and cargo. However, it would appear that there is a murderer aboard as passengers begin dying. It is not long before another threat rears its head when part of the cargo, giant seedpods are found burst as the result of an electrical overload. The scientists responsible for the seed pods insist they are empty husks but as more passengers and crew begin to die it would appear that something else is loose on board the ship...

Faced with charges he is unable to refute the Doctor is astonished when his old foe, the Master, comes to his defence. Proving that the Matrix can be breached and its contents corrupted this would appear to prove that the evidence in the Doctor's trial can be altered. However, what reason could the Master have for coming to the Doctor's aid? And not only that, but providing him with witnesses in the shape of Mel and Glitz? It would appear that the Doctor faces a threat even greater than the Master. This new foe could be the Doctor's undoing - a rival to the Master's own plans for destroying the him. A rival the Master would gladly see fall, perhaps even taking the Doctor with him. Now the Doctor must face his ultimate foe...