The story made up of episodes 9-12 is generally referred to as Terror of the Vervoids.

After a short recess to allow the Doctor to come to terms with Peri's death, the Valeyard rests his case for the prosecution. It is now the Doctor's turn to present a case for the defence. He announces that by showing the court an adventure from his own future, he hopes to demonstrate that he mends his ways. 

The Doctor is now travelling with a young girl named Melanie - a keep-fit fanatic who has him exercising and drinking carrot juice - and their latest adventure begins when the TARDIS picks up a distress call from someone aboard an intergalactic liner, the Hyperion III. 

The Hyperion III ferries between Mogar and Earth in the year 2986, and amongst its present cargo are precious metals from Mogar and a mysterious light-shielded hydroponic section containing several giant vegetable pods. A passenger, Grenville (Tony Scoggo), is recognised by one of his fellow travellers, Kimber (Arthur Hewlett), as being a man named Hallet. He dismisses this as a case of mistaken identity, but his actions are suspicious and he later disguises himself as a crew member in order to gain access to the cargo hold. 

Arriving on the Hyperion III, the Doctor and Mel are arrested as intruders. They meet the ship's Commodore, 'Tonker' Travers (Michael Craig), who is an old acquaintance of the Doctor's. Travers is sceptical of the Doctor's explanation for his arrival here and claims to know nothing of any mayday. However, he tells the ship's security officer, Rudge (Denys Hawthorne), to allow the two travellers the freedom of the passenger quarters - if the Doctor is up to no good, he will incriminate himself in time. 

The Doctor and Mel join the rest of the passengers, who include a group of botanists led by thremmatologist Professor Sarah Lasky (Honor Blackman). It is they who are responsible for the hydroponic section in the cargo hold, and also for a guarded isolation room which is off-limits to everyone else. 

Grenville disappears and one of his shoes is found by the ship's incinerator. The implication is that he has been murdered. The Doctor suggests that Mel investigate the hydroponic section on her own. 

The Doctor again tells the court that the Matrix is wrong, asserting that this section of evidence was different when he reviewed it earlier. He has a strong feeling that he is being manipulated and that the evidence is being tampered with. 

Mel is shown around the cargo hold by the ship's communications officer, Edwardes (Simon Slater) - who, to her horror, is electrocuted when he touches a metal grille surrounding the hydroponic section. The electrical discharge also causes creatures within the pods to start moving and ultimately to break out. A guard who arrives to investigate Edwardes' death, having been alerted by Mel, is killed by the creatures. 

The Valeyard sneeringly registers this as another death to the Doctor's credit. 

Also on board the liner are three Mogarians, natives of Mogar who have to wear special breathing apparatus to survive in the same atmosphere as humans, oxygen being poisonous to them. They berate the Commodore for steering the vessel too close to a black hole, and also complain about Earth's mining of Mogar for metal. One of the Mogarians later turns out to be Grenville/Hallet in disguise. An undercover agent and an old friend of the Doctor's, it was he who beamed the distress signal to the TARDIS. Before he can reveal his reasons for doing so, however, he is poisoned by persons unknown. 

Lasky and her assistants try to cover up the fact that the pods in the hydroponic section are now empty. The Doctor and Mel, however, are highly suspicious of the thremmatologist and trick their way into the guarded isolation room. There they find Ruth Baxter (Barbara Ward), another of the Professor's assistants, who is slowly turning into a mutant form of plant life. 

Mel manages to record on tape some alien voices which she has overheard plotting the destruction of animalkind. The tape is subsequently stolen, however, and she suspects that the culprit could have been the liner's stewardess, Janet (Yolande Palfrey). At the Doctor's suggestion, she goes to search Janet's cabin. The Doctor then makes for the liner's communications room and smashes the equipment with an axe. 

The Doctor again protests that this is not what really happened. 

While Mel is in Janet's room, it is entered and wrecked by one of the alien plant-creatures, or Vervoids. Another of the creatures overhears Bruchner (David Allister), a member of Lasky's team, plotting to destroy them, having realised the threat that they pose to the human race. The Vervoids determine that he should be the next to die. 

After burning the team's notes, Bruchner obtains a gun and heads for the flight deck. He manages to set the ship on a suicide course for the Black Hole of Tartarus before succumbing to a cloud of poisonous marsh gas emitted by a Vervoid in the air conditioning duct. The presence of the gas prevents the liner's human crew from entering the flight deck to alter course, but Rudge summons the two Mogarians, Atza (Sam Howard) and Ortezo (Leon Davis), who can do so without suffering any ill effects. 

It transpires that Rudge and the Mogarians have been planning all along to hijack the liner. Now that they have seized control of it, they refuse to hand it back to the Commodore. The Mogarians are angry about the human exploitation of their home planet, while Rudge is in it simply for the money - this is to be his last tour of duty. The Mogarians' plan goes awry, however, when an unseen figure enters the flight deck and throws acid on their face masks, allowing the liner's air to penetrate and suffocate them. With his allies dead, Rudge is easily overpowered. 

The Vervoids (Peppi Borza, Bob Appleby, Gess Whitfield, Paul Hillier, Bill Perrie, Jerry Manley) begin a reign of terror on the ship, systematically wiping out the human crew and passengers. 

Another of Lasky's assistants, Doland (Malcolm Tierney), is revealed to be behind the murder of Hallet and the Mogarians. He plans to bring the Vervoids to Earth, for use as cheap slave labour. However, he too is killed by the creatures. The Doctor realises that the liner's occupants are in a terminal situation: it is a case of kill or be killed. The Commodore asks for his help. 

The Doctor points out to the court that this proves his assistance was requested. He was not interfering. 

The Doctor realises that rather than try to kill the Vervoids, it would be better to encourage them to grow. There is in the cargo hold a metal called vionesium, which has properties similar to those of magnesium and emits a bright light when exposed to air. The Doctor tells the Commodore to switch off all the lights on the ship. This causes the Vervoids return to their lair, where the Doctor and Mel use vionesium bombs to expose them to intense light. The creatures' growth accelerates out of control and they turn brown and crumble to dust as their energy reserves are used up. 

As the Doctor completes his defence, the Valeyard states that the charge against him must again change. The Inquisitor agrees that Article 7 of Gallifreyan Law can be invoked. The Doctor now stands accused of genocide.

Synopsis from Doctor Who: The Sixth Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos