The Doctor is put on trail by the Time Lords again. The first of two events from his resent past is presented as evidence of his interference in the affairs of other worlds. In particular, his actions on planet Ravalox.
The Doctor finds that the subterranean UK Habitat is run by a cloistered robot named Drathro, whom the inhabitants call "The Immortal." Their black light energy converters are destabilizing, unaware that it's the result of two space pirates mucking about on the surface with designs on looting their dwelling.
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.
Having been put through a makeshift truth extractor, the Doctor appears damaged, apt to mimic the personalities of those with whom he has eye contact. He eventually abandons Peri and a gung-ho warrior king in favor of joining in with Sil and Dr. Crozier in the latest of their perverse projects.
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.
The first transfer is flawed, so Dr. Crozier needs to transfer Lord Kiv into another host body. Unfortunately, Peri meets all the requirements for the subsequent candidate. Since the Doctor's been helpful and has somewhat of a personal interest in Peri, he's permitted to locate an equally suitable substitute candidate, if he can. The prosecution rests.
A lethal booby-trap in the Hydroponic Center awakens the genetically engineered fruit pods in storage, and passengers and crewmen alike start disappearing without trace. There's a murderer on board and the Doctor means to find out who he or she is.
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 harboring 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.
So much ado by the Valeyard and the Master over the Doctor's death makes the Doctor wary of being made decoy for some other, truer target. Continuing in the Matrix itself, he may find both them and the answers he seeks.