When the Fourth Doctor takes Leela to visit an immense tree space station known as the Heligan Structure, little do they know that the tree has been asleep for centuries, dreaming of vengeance against a man in a blue box ... As the tree awakes, the Time Lord and his companion soon discover why they are such unwelcome guests.
A boy named Ven walks in the trunk-roads tasked to observe his society's food supply as the Justiciar's son. Ben begins to hear creaking noises from the central tree, which he despises. As Ven follows a swarm of the bees to the area's honey hive, the creaks from the tree begin to intensify until he begins to hear a new sound and sees a shining light. The place Ven was standing on was a spot where he had been when he was younger with his grandfather mourning the loss of some people. As the light begins to dim, a rectangular blue box appears provoking Ven to have a sudden rush of fear.
Inside, the Doctor with his long scarf declares that they've landed as Leela rushes out of the TARDIS swimming pool. The Doctor tells Leela that he took notice of how much she complained about missing the trees, in which Leela replies that she did not complain, and says that he has brought her to the Heligan Structure – "a tree; one enormous, genetically engineered tree, the size of a small moon" – which has been modified by Earth people in the 24th century through terraforming. Leela notes that the structure is not a tree due to its lifeless appearance, but The Doctor notes that the tree lives inside with a civilisation full of tree houses – "It's a space station, Leela. A wooden space station!"
While K9 recharges, the Doctor and Leela exit the TARDIS observing the wooden caves they materialised into. Leela turns around and finds a petrified Ven watching them, and the Doctor began to offer him a jelly baby. The Doctor introduces himself and Leela to Ven, and in return Ven introduces himself noting it is short for "Vengeance-Will-Be-Ours-When-the-Doctor-Dies-A-Thousand-Agonising-Deaths". The name provokes the Doctor's grin to fade.
As another tremble occurs in the forest, Leela sense that there is danger and walks back to the TARDIS, which has been entwined by the living wood of the tree. Leela asks the Doctor to do something, but he notes that his sonic screwdriver has no effect on wood. Leela slashes the wood with her knife, but there is no effect as Ven says that the two will never get their TARDIS back and they will die. Another trembles emerges causing a terrified Ven to fall into a pit filled with greenish sap, in which the Doctor responds by getting him out with his scarf. Behind the three, a girl and three men in armour try to take down the Doctor until the girl – Aggie – notes that it's the Doctor. The Doctor asks Aggie what her name was short for – "Agony-Without-End-Shall-Be-the-Doctor's-Punishment" – which provokes him to believe he and Leela aren't welcome to the Heligan Structure.
Aggie tells Ven that Chairman Ratisbon – the leader who would seek out vengeance for the people – sent her to find out what happened once the tree began to awake. Ven notes that the tree has profiled the prophecy of trapping the Doctor, but he expresses confusion when he mentions that he saved his life. Ven and Aggie take the Doctor and Leela to the Justiciar while the Doctor hears more trembling in which Leela translates to anger as the roots begins to unfold and expand.
In passages the of the Heligan Structure, commoners begin to spread news about the Doctor's arrival, yet the Doctor can't stop admiring them. Aggie tells the Doctor that the structure was stranded in space for roughly 900 years with no wreck occurring. Ven's mother greets the Doctor with a stern face informing him Director Sprawn – the leader – has designed the structure to lure the Doctor as revenge for what he did to Golrandonvar – a planet which Earth was colonising due to the Heligan trees. The Doctor doesn't remember Golrandonvar while Ven and Leela begin to defend the Doctor's good nature to the Justiciar, which she accepts as true. The Justiciar decides that she will bring up his good nature during the trial, but they are interrupted when an elder man looking for revenge – Chairman Ratisbon– declares that there should be no trial.
While the roots of the tree begin to infiltrate the TARDIS, the Justiciar begins to defend the use of a trial to Chairman Ratisbon, who begins to say that she is not fit to be a Justiciar. As Rotisbon's men begin to take the Doctor away, Leela, who has fleed from her guards which she speared, question the Justiciar believing that she was the leader, in which the Justiciar believed herself. After a crack was heard, a bunch of green, sharp-spined, claw-like roots began to emerge in the Justiciar's room from below. Leela realises that the roots can hear but not see, but she claimed that only the Doctor would know how to stop them, provoking Leela and the Justiciar to save the Doctor while Ven and Aggie go to the Hall of Justice.
Ratisbon brought the Doctor to the Chair – a chair constructed by early colonists to torture the person who was siting on it with its blades and acids. Before Rastibon could get the Doctor to take a seat, Aggie bursted in the room claiming there are vicious roots everywhere. The chairman initially dismissed it believing it was a trick by the Justiciar, but then he was snatched to death by the roots into the bottom of the tree. The Doctor escapes with Aggie revealing them to be spore-like creatures released by the tree for repopulation, but he further deduces that they were programmed to act like warriors. While they run away, Aggie is told by the men to kill the Doctor in which she responds by saying no and nearly spearing them until the Doctor prevents her.
At the Hall of Justice, the Doctor, Leela, the Justiciar, Ven, and Aggie meet up. There, the Doctor notes that there is a funny-looking statue in which the Justiciar claims to be him. Leela notes that the statue looks nothing like him as the statue depicts the man the colonists encountered 900 years ago – a man with two eyes, two ears, a distinctive nose wearing a bow tie, in which Leela calls young and handsome while the Doctor himself thinks he would never get caught wearing a bow tie. Ven then proceeds to say that this Doctor said "bow ties are cool", in which the Doctor believes is not cool. The Doctor then realises that the people are blaming one of his future regenerations on the spores, the revolt of Thara, and the exile from Golrandonvar, which the Doctor says hasn't happened in his timeline, yet.
While some men say that the Doctor should be killed to prevent their history from happening. The Doctor notes that none of what was happening would ever exist and everyone would vanish into a paradox. Another quake had emerged as the statue of the Doctor "swayed drunkenly, " and the Doctor agreed with Leela's statement about the trees being angry – a statement she believed the Doctor would dismiss due the unscientific language. The Doctor deduced that the there was a centre to the tree which sensed his arrival. In to the heart of the Heligan Structure, Ven led the Doctor into a cave that brought him to Director Sprawn.
The Doctor tells Sprawn that despite how little knowledge he knows of Golrandonvar, he believes that he ands fellow colonists were aggressive tyrants rather than victims of the Thara rebellion. Sprawn argues than the Thara opposed what they did to terraform their world, and they had to change the atmosphere to fit humans and exterminate the Thara – which the Doctor heavily disliked due to choice of words. The Doctor continues to deduced that Sprawn has kept the tree from spawning, provoking the spores to become aggressive. To bring the tree back to normal, the Doctor adjusted the chemical balance while Sprawn the spores and limbs turned him into a part of the tree.
The Doctor told the Justiciar that in ten years, the tree would be very habitable. As the humans watch the spores take flight across the sky (and Ven and Aggie hold hands), After slashing the roots on the TARDIS door, Leela tells the Doctor that she had a plenty amount of trees for a while, and the Doctor says he is interested in going to the sand-reefs of Phenostrus IV.
- Fourth Doctor
- K9 Mark I
- The Justiciar
- Chairman Ratisbon
- Director Sprawn
- Eleventh Doctor
- The Doctor and Leela have been to the crystalline cities of Ix.
- The Doctor notes that he does not like bow ties.
- While inquiring about Golrandonvar, the Doctor asks if it looked "a bit like a gravel pit," quipping, "You'd be amazed how many alien worlds look just like gravel pits." This is reference to the quarries that episodes of Doctor Who were filmed in during Tom Baker's time on the show.
- An audiobook of the story was read by Sophie Aldred.
- The story shares a great number of similarities with the plot of The Face of Evil, as both situations see the Doctor arrive in a location and learn that he is regarded as a villain by the locals due to a misinterpretation of past actions.
- Leela remembers seeing the steel hives of the Sun Makers of Pluto. (TV: The Sun Makers)
- The Doctor tells Leela that the sonic screwdriver "doesn't do wood." (TV: Silence in the Library)