Lieutenant Deral of the Ondrockan military is searching for one Major Koth in an underground cave system while his companion, Lieutenant Fraxin, keeps watch for Koth’s followers on the surface. Deral eventually finds Major Koth listening to a recording of his wife, wishing him well. Deral reluctantly shoots Koth, but his weapon has no effect -- and Koth shows Deral just how powerful he has become...

The Kro’ka has sent the Doctor, Charley and C’rizz to a tropical jungle following their visit to Light City. The Doctor senses that he and his companions are drawing closer to the missing TARDIS, but he still does not understand the nature of the zones they’re crossing, or how and why the interzone barriers have been created. When he and his friends find a waterfall emptying into a small pond, Charley enthusiastically dives in for her first shower in two days. The Doctor and C’rizz explore further, and, a short distance away, they find the remains of a hover-skimmer and a skeletal body coated in moist soil -- which is odd, as the ground about them is bone dry and the signs indicate that the skimmer crashed quite recently.

Two military officers, Captain Tysus and Sergeant Bryn, capture the Doctor and C’rizz and question them about the dead body. Tysus is willing to kill them simply for expediency’s sake, even if they have nothing to do with the death; she is searching for Major Koth, a former war hero who has become the leader of a terrorist cell, and she can’t waste time on side issues. Charley watches from hiding as the Doctor manages to convince Tysus that he and C’rizz are innocent travellers. He also points out a nearby cave mouth, and suggests that it would be logical to hide a secret army camp underground near a supply of fresh water. Tysus orders Bryn to keep an eye on C’rizz while she and the Doctor investigate the caves. Before entering, the Doctor gives Tysus a locket which he found on the body, proof that it is the body of Lieutenant Fraxin -- which has almost entirely decomposed though he only vanished two days ago.

Underground, Sub-Commander Quillian detects movement on the surface and reports this to Commander Vayla. She sends him to investigate, and he finds Charley watching the others, unaware that she’s standing perilously close to a toxic reaver plant. He warns her to move away from it, but is too late; the plant lashes out, stinging her hand. Quillian quickly heats the water in his flask to boiling point and tells Charley to stick her hand inside to boil out the poison; otherwise, she’ll be paralysed for life. She does so, and accompanies Quillian into the caves for treatment.

Meanwhile, Vayla reports the incident to Koth, and, in light of the recent military incursions, suggest that they move the camp elsewhere. Koth assures her that there’s no need to do so, as they are close to achieving their objective. As he speaks, Koth suddenly convulses, sensing that a new and interesting being has just entered the caves. This is the Doctor, who also convulses briefly, sensing a powerful, raw feeling of rage emanating from the cave system. However, when he questions Tysus, she claims that her target, Major Koth, is not telepathic.

As Tysus tells the Doctor about Koth, C’rizz learns the story from Bryn. Terrorists have been attacking Ondrockan civilians out of anger at the planet’s refusal to share its affluence, and Koth was a decorated hero in the war against them. While he was off-world on a mission, however, terrorists released a virulent plague on the island city of Beytara, and the government atomised the island to ensure that the plague didn’t spread to the rest of the planet. Major Koth’s wife and children were lost, and he was not informed because the government didn’t wish to distract him from his work. When Koth learned what had happened to his family, he denounced the government for its failure to protect its citizens and went into hiding on this planet, which Bryn and Tysus believe to be Sartaris. It seems he has since decided to fight the war on his own, and since many scientists and key military personnel have defected to Koth’s private army, the government has been forced to take notice. But even Tysus and Bryn don’t realise just how dangerous Koth has become since arriving on this planet...

Quillian reports to Vayla that at least two of the newcomers appear to be Ondrockan military, but he’s not sure about the others. Vayla, who’s expecting a new recruit by the name of Doran to arrive, fears that the military officers have arrested him and orders Quillian to take a patrol out to find and rescue him. Before going, Quillian asks what Koth had to say to her, and Vayla assures him that good news is forthcoming. Meanwhile, Charley’s hand is treated by Byzar Janto, who is much more cynical about the revolution than his compatriots. He is not in fact the base’s medic; he’s just acting as one because the new medical officer has not yet arrived. Oddly, Janto can’t quite recall what happened to the last one.

As Tysus and the Doctor proceed through the strangely luminescent caves, they encounter a swarm of grellicks, rodents native to Ondrocka -- and find Deral’s body, which, like Fraxin’s, has been stripped of its flesh and is covered in rich, moist soil. Tysus tries to contact Bryn to warn him of the danger, but has trouble contacting him from this far beneath the surface; nevertheless, she insists upon proceeding, determined to find positive evidence that Koth is based in these caves before she retreats to call in reinforcements. Unfortunately, she gets her positive proof when Quillian and his men surround her and the Doctor.

On the surface, Bryn tries and fails to contact Tysus. Fearing that whatever killed Fraxin might still be about, C’rizz now admits to Bryn that he has another companion, Charlotte Pollard. Bryn sets off to look for her -- but someone else finds him instead, and his weapon has no effect on the newcomer. Meanwhile, deep beneath the surface, as Koth listens to the Doctor, two other voices speak to him of what they can sense in the Doctor’s mind. Despite the tense situation, the Doctor shows no fear -- and the voices decide they must show him what fear really means.

The Doctor manages to get through to Bryn, who hesitates just long enough for Janto to intervene and suggest that the Doctor may be Doran, a strategist whose arrival they’ve been expecting. Koth thus postpones the Doctor’s execution until his identity can be verified. Since he and Charley obviously know each other, they are locked up together, in a cave sealed behind a defence screen which will pulverise them if they try to step through it. However, even Vayla is concerned by the impromptu execution of Tysus, and the Doctor is particularly worried about Bryn, who just killed his own commanding officer without hesitation or a flicker of emotion. Whatever force the Doctor felt as he entered these caves, he’s certain that these strangely dispirited freedom fighters are under its influence.

Quillian shows Bryn to his new quarters, where Bryn sits down to rest, unsure what he’s doing here or why the woman he just killed seemed so familiar. Quillian believes that this is just the natural disorientation all new recruits suffer, and admits that even he isn’t quite sure how long he’s been down here. Meanwhile, Vayla questions C’rizz and threatens to administer a truth drug to get answers out of him, even though he’s quite openly agreeing to answer all of her questions anyway. Janto intervenes once more, and Vayla realises that she’s being uncharacteristically suspicious and hostile. She thus stands down, but warns C’rizz that she’ll kill him herself if he betrays her trust.

The Doctor tries to deactivate the force field around his cell, and eventually succeeds -- or so he assumes. Charley reluctantly accompanies him, although she’s realised that she doesn’t want to escape; as she points out, she and the Doctor usually side with rebels against the oppressive governments. The Doctor, however, is disturbed by the attitude of these particular rebels, and he soon finds that the armoury and the lighting in the caves is shoddily constructed and poorly maintained. The walls of the cave are moist and sting Charley’s skin when she touches them; and though she sees a figure watching them from the distance, when she and the Doctor investigate they see only a pile of loose soil. They also encounter another swarm of grellicks, crawling over each other in a demented attempt to burrow into the soil. As the Doctor puzzles out the mystery, he is unaware that Koth and the two voices with him are observing his and Charley’s every movement; it was in fact Koth who deactivated the force field, releasing the Doctor from his cell.

Quillian is forced to decrease the army’s food rations for a time, but Koth appears and gives him a pep talk to boost his morale. Quillian takes the opportunity to question Koth about Vayla’s erratic leadership, and also about what’s going on in the other camps; however, Koth glosses over the questions, and later, while speaking with Janto, Quillian seems to have forgotten that he ever asked them. However, Janto is less idealistic and less willing to take Koth’s claims at face value, and he’s starting to wonder why the people who’ve been promoted and moved on to the other camps have never reported back...

Corporal Orvik discovers that the Doctor and Charley have escaped, and Vayla sends Quillian and Bryn out to find them and prevent them from getting away. While Janto scans the caves for the fugitives’ life signs, C’rizz tries to convince Vayla that the Doctor and Charley pose no threat, but he’s talking in vain; once again, it seems that his training in the ways of peace has failed to prepare him for life in the wider universe. Vayla tells C’rizz about her sister, who was still in Beytara when the virus was released. Suza called her sister for help on the videophone, and Vayla was forced to watch the flesh melt away from her sister’s body, unable to do anything. This is why she will not permit the Doctor and Charley, innocent or not, to leave with knowledge of the camp’s location.

The Doctor and Charley hear the sounds of pursuit, and follow an underground stream to a dead end. Certain that the water must be going somewhere, the Doctor dives in, even though Charley points out that the “water” is the colour of blood. She still doesn’t believe they should be fleeing from these people, but she reluctantly follows the Doctor in when he reminds her that the rebels somehow managed, within minutes, to brainwash a trained soldier into executing his own commanding officer. When Quillian and Bryn arrive, there’s no sign of either the Doctor or Charley, but when Janto picks up their life signs in an adjacent cavern, Quillian realises what they must have done and dives into the pool after them.

Fortunately for Charley, the pool is just water again. Quillian forces her and the Doctor to swim back out of the caverns, and reports Bryn’s death to Vayla. Vayla passes the report on to Koth, who accompanies her back to the main camp to question Quillian and the Doctor. Quillian accuses the Doctor of murdering Bryn, but he can’t quite remember how it happened, and when Janto speaks up on Charley’s behalf, Koth unexpectedly drops the whole issue and gives the Doctor and Charley the run of the camp. Vayla agrees to do as Koth commands, which is no more than the Doctor had expected of her -- but Charley, unexpectedly sick of the Doctor’s taunting, snaps and tells Vayla that the Doctor is indeed not Doran. Koth and the two voices observe the Doctor’s confusion, and realise that they’ve managed to hook him through his curiosity. Meanwhile, Quillian storms off to eat dinner, still convinced that the Doctor and Charley are somehow responsible for Bryn’s death, even if he can’t quite recall how.

C’rizz is shocked by Charley’s betrayal of the Doctor, but so is she; is it that the Doctor has become harsher and more judgemental in this Universe, or is there some other reason she’s turned on him? C’rizz leaves her to her musing while he participates in weapons training; soon, he is handling a gun like a seasoned pro, which Charley finds odd, as he was brought up in the ways of peace. Janto, observing this, advises Charley to leave the camp while she still can, before the despair and need for revenge consumes her and she ends up as lifeless as all the other rebels.

The Doctor questions Vayla about her willingness to let him walk freely about the camp, and she admits that she’s too tired to care any more. Intrigued, the Doctor decides to analyse the fungus which the rebels have been using for food rations, but as he works, Major Koth arrives and reveals that he knows the Doctor to be a “Time Lord” -- even though he doesn’t understand exactly what “Time” is. Koth can sense the emptiness within the Doctor, who has been cut off from everything he knows and holds dear; nevertheless, he claims that the Doctor and his friends are free to leave any time they wish. The Doctor vows to remain and stop him from turning these people’s despair and fear into a weapon for his own ends, which is just what Koth expected him to do.

Quillian waylays Vayla as she returns to her quarters; he’s convinced that Koth has given her more than the vague promises she’s passed on, and demands to know why she’s keeping secrets from him. However, Vayla no longer remember what Koth told her, or indeed how many times she’s visited him today. When Quillian presses her for an answer, she collapses, finally overwhelmed by exhaustion. Koth arrives and offers to take Vayla back to his quarters, claiming that the caves have certain regenerative properties. Vayla is too weak to understand what’s happening to her, even when Koth takes her to his private island and lays her to rest in a bed of soil. Soon she is beyond caring; the voices which have been speaking to Koth consume her, and she cannot resist, as her guilt over her sister’s death has left her with no desire to live.

Janto is peeved to find the Doctor meddling in his laboratory, but the Doctor soon convinces him to admit that he too has doubts about what’s happening here. When the Doctor finishes analysing the fungus, he finds that it does not possess any mood- or mind-altering properties; however, it’s a suspiciously well-balanced nutritional compound. When Charley arrives to find the Doctor musing aloud on the nature of the enemy, she loses her temper again and storms out, convinced that the Doctor is looking for evil where there is none -- just as the Doctor is now convinced that she too is being affected by whatever’s at work within the caves. Janto, realising that the Doctor is deeply concerned for his friends, advises him to pull himself together and act on his feelings. Janto joined Koth’s army because he lost his wife, but he hasn’t sunk into self-pity and despair like the others in the camp. Nevertheless, he’s found it impossible to leave -- and when pressed, the Doctor realises that he too never intended to leave the caverns, even when he escaped earlier. He had perfectly good reasons for wanting to remain, or at least that’s what he thought at the time... Realising that he too may have been affected by the influence in the caves, the Doctor decides to confront Koth in person on his isolated underground island and try to break whatever hold he has over the rest of his army.

C’rizz finds Charley sitting alone in the main cavern, struggling to understand why she’s so upset with the Doctor. She’s starting to realise that she doesn’t really have a reason. C’rizz admits that he’s also unsure why he wants to join Koth’s army and stay in these caverns; he joined the Doctor and Charley to see more of the outside universe and learn about other cultures and beliefs, not to fight in other people’s wars. It’s as if he is being transformed into a weapon. Charley finally realises that the Doctor was right; something is terribly wrong here, and both she and C’rizz are being affected by it.

The Doctor finally realises the truth: the entire cave system is one gigantic living organism, and the soil and water are its digestive system. In its natural state, it feeds on local wildlife, using its low-grade telepathic abilities to lure them in like a gigantic flytrap. But when Koth arrived, seeking solitude after his great loss, the creature consumed him and became overwhelmed by the grief and anger within his mind. Koth and the creature bonded to form a new, symbiotic entity, with the ability to create temporary bodies for itself out of the soil of the caves. Ever since Koth arrived, the creature has been luring new recruits to this planet to join an army that does not in fact exist, using its avatars to keep the recruits from asking too many questions, and stringing them along while the organism works away at their minds and breaks down their resistance until it is ready to eat them.

Janto is horrified, even more so when the organism reveals that it never did anything to his mind; the others stayed because it prevented them from leaving, but Janto stayed because he could think of no reason to return home. The organism drives Janto away, attacking his mind once again and forcing him to retreat back to the camp. It then turns on the Doctor, who tries to communicate with the spark of Major Koth, the war hero who came to this planet with no evil intentions. He fails, and the organism prepares to break his resistance by threatening his friends.

Back in the camp, Charley and C’rizz prepare to search for the Doctor, but the organism influences Quillian to confront them, apparently convinced that they’re peace activists sent to sabotage Koth’s work from within. Just as he’s about to shoot them both, the organism releases him from its influence, and he walks off, unaware that anything strange has happened. C’rizz then accuses Charley of collaborating with Quillian in order to lead him and the Doctor into a trap, but again, the organism releases him and he recovers with little memory of what’s just happened. Janto then arrives and ushers Charley and C’rizz out of the camp, explaining the truth as they run.

The organism, having made its point, demands that the Doctor lower his defences and let it in. He tries instead to reach out to it, convinced that the creature is in pain and that its two voices are the symptom of a split personality. But Koth attacks the Doctor’s confidence, claiming that the Doctor had become complacent in his old, familiar Universe, and that here he’s isolated, alone and uncertain. The Doctor remains unfazed, but the organism soon realises that he’s trying to keep it distracted while his friends escape -- and it thus turns on them once again, determined to break his resistance. Janto, Charley and C’rizz are thus attacked by a swarm of grellicks as they try to flee, and though C’rizz tries to shoot at the pack, he’s no longer under Koth’s influence and is no longer as proficient a shooter as he appeared back at the camp. Nevertheless, Charley is disturbed by his growing aptitude for violence. At the last moment, the grellicks turn and flee, but only because the organism is preparing another attack. Soil spills out of the walls and takes the form of Major Koth -- in not just one body, but several. And Janto’s and C’rizz’s weapons have no effect on the facsimiles.

The Doctor warns the organism that killing his friends will not break him, and finally realises why it is trying so hard to do so. It has drawn all of the nourishment it can from Koth’s mind and body, and he is dying -- but the organism has become addicted to the rush of emotion that it draws from sentient minds, and thus wants another to take Koth’s place. The Doctor refuses to do so, insisting that the conditions that created this hybrid were a freakish accident -- albeit a suspiciously unlikely one. Koth then claims to have a surprise, and much to the Doctor’s shock, the TARDIS materialises before his eyes -- but when he tries to open it up, his key does not move in the lock. Apparently, the creature’s telepathy is not only powerful enough to have drawn the TARDIS to it when the TARDIS first materialised, but also to keep the Doctor locked out. The Doctor thus gives in and agrees to take Koth’s place, but only on condition that the organism release the members of Koth’s army that it’s been holding captive. The creature agrees to do so, and separates itself from Koth’s mind.

The crowd of faux-Koths surrounding Janto, Charley and C’rizz dissolve back into soil. But, freed from his link with the creature and finally able to speak to the Doctor as himself, Koth reveals that the Doctor’s friends are now in even greater danger. The Doctor understands Vayla’s warning too late; the organism itself is a child, experiencing real grief directly for the first time, and when it loses Koth it will lash out in fury at this new, painful emotion. As Koth dies, he warns the Doctor that this creature is not native to Sartaris; somehow it was transplanted here, as was Koth. This entire situation was organised by some other force, but if Koth knows who or what is responsible, the secret dies with him. As the Doctor had feared, the creature cannot cope with Koth’s absence, and it demands that the Doctor take Koth’s place -- and when the Doctor insists that he cannot replace Koth, the organism lashes out in rage, threatening to consume every living thing within itself.

Back at the camp, Corporal Orvik reports to Quillian that the tunnels are suddenly filling with soil -- which then transforms itself into facsimiles of Major Koth. Their touch is lethal, and as Quillian loses contact with the screaming Orvik, a facsimile enters the communications centre and strikes Quillian down as well. Elsewhere in the caverns, Charley, C’rizz and Janto find their way blocked by the acidic soil, and Janto is horribly burned when he tries to dig through only to have more soil spill out of the tunnel wall atop him. The Doctor finally gives in and merges with the organism, putting an end to the slaughter, and the dying Quillian manages to warn his people to evacuate before he collapses.

The soil which was attacking Janto transforms itself into a duplicate of the Doctor, who directs his friends to Koth’s cave and the waiting TARDIS. Unfortunately, he has a problem: if he tries to disconnect from the organism, it will flood the chamber with soil, killing them all. Janto therefore offers himself up in the Doctor’s place; he’s had no reason to live since his wife died on Beytara, and he feels that the Doctor and his friends deserve a chance to live. The Doctor is unable to convince him otherwise, and reluctantly accepts Janto’s sacrifice. He and Janto switch places -- but the TARDIS suddenly dematerialises, and the Doctor realises that there’s far more going on here than he’d suspected. Meanwhile, the organism merges with Janto, but it’s unprepared for what happens next: Koth’s grief was born out of anger and pain at his loss, but Janto’s grief was born out of compassion and love for his wife. This is too much for the organism to handle, and the new hybrid, overwhelmed by the strength of Janto’s emotion, dies of a broken heart. As he dies, Janto urges the Doctor and his friends to leave and solve the remaining mysteries of this Universe; perhaps the Doctor can be a Lord here once again.