The year is 2673, and the human colony on Tairngaire has started a secondary colony of its own on the forest world of Arden. But odd things are beginning to happen on both worlds. Surveyor Donal Robson awakens with a start in the forest of Arden, convinced that he is drowning -- and then immediately forgets that he ever felt anything wrong. Lyn Sorren, science co-ordinator at Touchstone Base, receives a call from her counterpart at Oberon asking for the return of some odd black minerals O’Valle had sent to Touchstone for analysis; however, O’Valle can’t explain why the “oberonite” is so important to him, and in any case Sorren has already sent the samples to the University of New Byzantium on Tairngaire. Shortly afterwards, a young security guard at the University is injured by intruders who attempt to steal the strange black gems from Arden…

The Doctor accidentally passes on some of his melancholy mood to Ace and Benny while sorting his memories through the telepathic circuits. The experience reminds Ace that it’s her birthday, and the Doctor offers to take her to the peaceful Tairngaire to relax. They materialise in a sculpture park in New Byzantium, and despite herself, Ace eventually finds herself enjoying the holiday. But someone else on Tairngaire is having a much less relaxing day. Gerry Ostman, who has just returned from Arden, finds himself suffering periodic blackouts and losses of memory during which he becomes convinced that he is being followed. While shopping in in the Lantern Market, Ace sees two men follow the terrified Ostman into a side street. She arrives too late to stop them from shooting Ostman through the chest, but drives them off with her homemade sweet-bombs, which appear to be harmless candies until they are activated by saliva. Ostman is already dying -- but as Ace studies the body, a small animal crawls out of the gaping wound in his chest, and dies.

Police Inspector Quillon takes the Doctor and his companions to the station to explain how they managed to arrive on the planet without passing through customs. A military taskforce arrives to take them away for a more detailed interrogation, but the Doctor and Ace become suspicious when their escort also picks up Ostman’s body, which was to have been examined by the police themselves. When the Doctor asks Lieutenant Tesseni about his last posting, the lieutenant hesitates and contradicts himself while answering the question, and Ace therefore uses her remaining sweet-bombs to blow open the back of the van so they can escape. As the Doctor and his friends flee, Quillon arrives with the real military taskforce, who open fire on the impostors -- and although the impostors are not affected by the human weapons, they realise that they are outnumbered and incinerate themselves to avoid being captured.

The city council convenes an emergency meeting, at which Marshal Talevara announces that his trusted aide Major Brandel authorised the despatch of the taskforce which attempted to kidnap the Doctor -- and that Brandel has since vanished. It appears that the government and military forces have been infiltrated by duplicates with an unknown agenda. The Doctor offers expert assistance to deal with the crisis, and provides City Prefect Annis Delray with credentials which cover several centuries. Delray and Talevara accept his offer of help, and the Doctor sends Ace back to the TARDIS with two of Quillon’s men to fetch the equipment he will need for his investigation. She does so, but is attacked by duplicates when she emerges from the TARDIS, and although she escapes by posing amidst a set of marble figures in the sculpture park, the duplicates steal the TARDIS while she is avoiding them.

The Doctor finds that all known duplicates had recently visited the colony on Arden and had not undergone medical testing since. When Ostman’s duplicate body is studied, no incendiary devices are found, but the scientist Strek does find an odd ceramic residue in its “brain”. The Doctor recognises it, and when he studies the black gems which were nearly stolen from the University his suspicions are confirmed. The duplicates are controlled with hypergems, which resonate in subspace and are capable of instantaneous transmission across astronomic distances. Even if the controlling intelligence is on Arden, it may already be aware that its duplicates have been discovered. Marshal Talevara insists that action be taken immediately, and although the Doctor is reluctant to provoke a counter-attack until he knows what he’s up against, he has no choice but to provide Talevara with a list of city councellors who have recently cancelled routine medical examinations after returning from Arden. The councillors are stunned and taken to the laboratories, where four of them are proven to be duplicates -- but the creatures living within them have no apparent intelligence of their own, which seems to indicate that they belong to a hive with a group mind.

As the Doctor had feared, the duplicates spring into action immediately upon realising that they are under attack. The soldiers at the military dockyards are caught off guard when trusted officers suddenly turn on their fellows and make off with two ships, opening fire on the yards as they flee and putting most of Tairngaire’s fleet out of action. Fortunately, a duplicate on the experimental ship Broadsword is exposed and restrained before she can sabotage the ship, and although she incinerates herself to avoid capture, the Broadsword remains undamaged. The duplicates on Arden then seize control of the colony, and put their bewildered colleagues and friends to work in the forest. The colonists at Oberon are forced to mine more hypergem ore, while those at Touchstone are set to work clearing space in the forest.

The well-planned attack suggests that the duplicates are prepared for all eventualities, and since reinforcements will not arrive from Earth for fifteen days, this in turn suggests that their plan will be complete by then. Talevara thus sends the Broadsword to Arden, and the Doctor, Ace, and Benny accompany the crew along with Quillon, Strek and a number of specialist advisors. The five-day journey is spent training and preparing; Ace has a fling with Marine Sergeant Santony, the Doctor helps to build a device which will distinguish between duplicates and ordinary humans, and Benny learns more about the ship itself, including the emergency solar sail. Meanwhile, the duplicates continue to work their slaves to exhaustion, and kill any who are injured and unable to work. The Atlas arrives at Touchstone with a number of objects like kilns, made of a smooth black material. The felled trees are fed into the kilns, and as they burn, the kilns begin to grow.

Upon arriving at Arden, the Broadsword scans the surface for transmissions, which seem to indicate that the takeover is contained to the two major colony towns. The Doctor’s hopes for peaceful contact are dashed when the Adamant locates them and attacks immediately, but the humans defeat their enemies with an untested new weapon which enters the Adamant’s drive core through the unshielded engine vents, thus blowing up the ship. Further surveillance pictures indicate that the skystation has been stripped of vital technology and abandoned, but when a drone is sent to investigate it triggers a boobytrap which destroys the skystation and all evidence of what was removed.

The Doctor, Ace and Benny accompany the landing parties, but as they set off the Broadsword is attacked by a matte black ship composed partly of bits scavenged from the skystation. As the crew of the Broadsword struggles to fight the impossibly maneuverable black craft, the landing parties are attacked by the duplicate-controlled Mercury, and many are killed before Kim Talevara -- the Marshal’s grand-daughter -- deliberately rams the enemy ship to give the others time to reach the surface. The Broadsword is forced to retreat, and the surviving Marines find that they are on their own. Since almost half of their party has been killed, they abandon their original plan to split up and investigate both colonies, and instead make their way towards Touchstone to investigate the kilns. But to the Doctor’s and Benny’s concern, Ace is amongst the missing. Meanwhile, the crew of the Broadsword analyse the data from their battle and discover that the black ship must be an autonomous entity with no crew, made of a sort of superdense carbon bond. Logic suggests that the matte black kilns at Touchstone are made of the same material -- but why do the duplicates require it on such a scale?

The injured Ace awakens to find herself in a nest of Shenn, intelligent natives of Arden and creators of the duplicates. These Shenn are friendly, however, and have rescued not only Ace but Kim Talevara as well. The Shenn were wary of the human colonists when they first arrived on Arden, and chose not to advertise their presence; however, these Shenn recently discovered that a nest in the mountains has been making duplicates and infiltrating human society. The Shenn from the friendly nest built the duplicate of Gerry Ostman to investigate the activities of the mounain-Shenn; the real Ostman is still in this nest, as the death of his duplicate has sent him into a state of shock. The Shenn have learned that their brethren are under the control of a voice from the sky, which calls itself Umbra. The duplicates’ brains are linked to their originals with hypergems, and thus think exactly as the originals do; the mountain-Shenn only take control of the body when their agenda conflicts with that of the original brain. The duplicates are thus unaware that anything unusual is occurring, even as they kill their former friends. Umbra must be stopped, and since the landing party’s journey to Touchstone will take two days, Ace convinces the Shenn to grow duplicates of herself and Kim so they can rejoin the fight without waiting for their injuries to heal.

The Doctor is unwilling to destroy that which he does not understand, but since it seems that the kilns are central to the duplicates’ agenda, the Marines decide that they have no choice but to take them out. Benny points out that the detritus emerging from the kilns is flammable, and the Marines thus set fire to it, causing a distraction which enables them to infiltrate the duplicates’ forces. By the time the duplicates realise what’s happening, the Marines are in a position to attack. Meanwhile, Ace and Kim’s duplicates attack the mountain-Shenn, breaking their control over the duplicates. The Shenn within the duplicates emerge and flee when their bond to the nest is broken, and the duplicates finally realise what they have been doing. But as the Doctor tries to calm down the shocked duplicates and their angry victims, the Marines discover that the kilns are starting to crack open. Santony tries to destroy them, but fails; the process has become self-sustaining, and vast clouds of sentient carbon dust pour out of the kilns and consume all in their path, generating piezoelectric bolts to kill anyone who gets in their way.

The survivors retreat to Touchstone as the shadowforms burn more trees to provide themselves with more carbon with which to grow. All of Touchstone’s heavy artillery was being used by the duplicates and is thus within shadowform territory; Ace and Kim thus accompany Santony to Oberon to fetch the artillery there. The shadowforms attack Touchstone, but the Doctor drives them off with a chemical spray which bonds to their carbon and dissipates the stored electrical charge, reducing the shadows to mere soot. When the attacking shadowform regroups and attacks again, it breaches the base and kills Sorren -- but in doing so it overextends itself, exposing its core. The Doctor connects a ground wire to his umbrella to earth the shadowform’s electrical bolts, and thus manages to reach the core and destroy it. Ace, Kim and Santony arrive with artillery from Oberon and drive off the attacking shadowforms, but before they can celebrate victory the black ship returns. The artillery is destroyed, Santony is killed and Kim’s duplicate body is destroyed, but the black ship allows the others to live and watch as the Atlas takes off, taking the shadowforms and hypergem ore to safety. The Doctor considers this to be the act of a childish and petty mind. Before the black ship can destroy its enemies, the Broadsword returns; using the data gathered from the previous attack, the crew has modified the Doctor’s duplicate detector to block the hypergem resonance spectrum, and they are thus able to disable the black ship and destroy it.

The Doctor identifies the enemy, Umbra, as an asteroid in a fixed orbit around Arden’s sun, with one permanently dark and one permanently light side. The potential difference between the carbon atoms on either side has resulted in photoelectrical activity, thought, and the evolution of a unique life form. But Umbra has developed in isolation, and it is greedy and immature, regarding other life as unimportant and wanting only to grow. The Doctor tries to communicate with it, but when he tells it that it will have to limit its growth until it has learned to co-exist with others, it petulantly responds to what it perceives as a threat. Before leaving Tairngaire, its duplicates planted shadowform seeds in the oil fields beneath New Byzantium, and Umbra now activates them. The young guard who prevented the theft of the hypergem ore is killed as the shadowforms burst out from beneath the University, and as the shadows sweep across the city, killing everyone they encounter, the Doctor reluctantly concedes that they now have no choice but to kill Umbra in self-defense.

The Broadsword thus sets off for the asteroid, but the crew has forgotten Umbra’s ability to control the minds of the mountain-Shenn -- and as they draw nearer to Umbra, it takes over their minds as well. Only Ace is unaffected, since she is still in a duplicate body and her actual brain is back on Arden. She manages to snap the Doctor free of Umbra’s control, and they go to the bridge, only to find that the crew have disabled weapons control. As the Doctor tries to restore power to the weapons, Umbra turns the crew on him and Ace, and Ace is forced to shoot her friends, even though she knows they aren’t responsible for their actions. Delighted by her predicament, Umbra concentrates on attacking her, but while it is occupied its control over the others slips. Benny and Quillon head for the bridge, where Quillon pulls out a stun gun -- and Ace instinctively shoots him dead even as he sweeps the bridge with it. As their attackers collapse, stunned, the Doctor and Benny unfold the ship’s emergency solar sail and throw the asteroid into shadow. The photoelectric reaction between the light and dark sides of the asteroid ceases, and Umbra dies, pleading with them to restore the light.

With Umbra’s death the shadowforms on Tairngaire collapse into dust. The TARDIS is found on the asteroid, just another object which Umbra treated as a toy. Despite the Doctor’s assurance that she had no choice but to act as she did, Ace still blames herself for the deaths on the bridge -- and she will never know whether Quillon had shaken off Umbra’s control when she shot him. As things start to return to normal, the Shenn agree to work together with the humans to repair the damage caused to Arden, and the Doctor decides to hop three weeks into the future so Ace can pick up her healed body from the Shenn nest. Once this is done, however, he intends to take another holiday -- without Benny or Ace along.