The Doctor is taken "out of time" by the Time Lords and made to face an inquiry into his meddling in the affairs of others, overseen by the Inquisitor. The prosecutor, the Valeyard, soon has the proceedings upgraded to a trial for the Doctor's life. Evidence takes the form of recordings of the Doctor's recent adventures, beginning with his visit to the mysterious world of Ravalox and an encounter with Andromedan space pirates...

The Doctor has an appointment with the Immortal, while Peri finds herself caught up with Glitz and the Tribe of the Free. Meanwhile, Merdeen begins to question all he believes.

The Doctor escapes to rejoin Peri on the surface but shortly becomes the prisoner of a surface-dwelling tribe called The Free. Ravalox isn't Ravalox after all, but before the Doctor can learn much more an irresistible agent from UK Habitat comes to fetch him back.

All those on Ravolox are in exponentially greater peril than anyone can comprehend. If anything in the entire universe is to survive, it may come down to the Doctor arguing against machine logic over the value of life.

The Doctor's trial continues. The Valeyard's next piece of evidence for the prosecution concerns the Doctor's recent trip to Thoros Beta. Though originally investigating arms dealing, the Doctor and Peri become embroiled in their old enemy Sil's alarming neurological experiments...

The scientist Crozier keeps making empty promises and Yrcanos and Peri are seemingly betrayed by the addled Doctor who is sure the Matrix is being manipulated...

While the Doctor helps Dr. Crozier transfer Lord Kiv's brain into a new host skull, Peri accompanies King Yrcanos as he searches for the Alpha Resistance fighters whom he feels, most certainly, will follow him into glorious battle against the Mentors and the Doctor.

As the Possidor Ambassador visits, Sil is appalled to realise Crozier has selected Peri to be the Kiv's new host body - a move Yrcanos takes exception to with devastating results.

As the Hyperion III continues its journey, more mysterious deaths occur.

A course change that takes the Hyperion III closer to a black hole could prove unwise when there are so many aboard ship with hidden agendas. Disappearances continue, a murderer remains at large, and one person finally crumbles under the strain of harbouring a guilty secret.

With factions vying for control of the ship, the Vervoids are found to be responsible for the many disappearances. Only the Doctor sees the fundamental but missed point as to why they can't be reasoned with or why they can't be allowed to arrive on Earth.

The Valeyard's true identity is revealed and the trial aborted, but the Doctor and Mel must pursue his new enemy into the Matrix itself, where nothing is quite what is seems…

The final part of this epic adventure. The Doctor and the Valeyard have entered the world of the Matrix. Can the Doctor defeat the evil incarnation of himself ?