The Doctor takes his companions for a picnic in a swamp within the TARDIS, to give Chris and Roz a chance to acclimatise to their new home and ensure that Chris has fully recovered from the effects of icaron contamination. The picnic is interrupted when the TARDIS picks up a distress call, but as the Doctor starts to materialise in response he realises, too late, that he and his companions each saw a different signal. The TARDIS has been lured into the detonation zone of a reality bomb built by former enemies of the Time Lords who have since been erased from existence; somehow, this bomb remained active, and when it explodes, the TARDIS is all but destroyed and the remains are sent spinning out of control through the Vortex.

Elsewhere, the inhabitants of a very odd System are under siege by the shape-shifting Sloathes of Planet X, a world which collided with the System some time ago and got stuck. The Sun Samauri Leetha t’Zhan of Aneas believes herself to be the Chosen One, whose quest to recover the Lost Eyes of the Schirron will restore peace to the System; unfortunately, she is taken captive by the Sloathes before her quest even begins. The Sloathe ship, however, is attacked by pirates led by the infamous Nathan li Shao, and in the course of the ensuing battle, Leetha is exposed to hallucinogenic gases and loses the papers which purport to describe the location of the Eyes and the dangers which face those intrepid enough to seek them out. Elsewhere, the Sloathe Captain Trankor Lep eats out part of the battlecruiser, which is itself a giant Sloathe, and hides within its structure. When li Shao arrives to rescue the prisoners, Lep ambushes him -- and the thing which really controls the System sees all of its carefully laid plans falling apart. Desperate, it reaches into the Vortex, grabs the first thing it can find and throws it at Lep…

The damaged TARDIS thus materialises inside Lep’s body, splattering it everywhere, and the deranged Doctor rushes out of the ship and then passes out. Benny follows him, but also loses consciousness due to the effect of the hallucinogens. The TARDIS uses its brief moment of existence to orient itself and get to Planet X, where it materialises fully and begins to heal. Roz and Chris emerge to explore, only to be captured by the Sloathes and put to work with their other slaves, sorting the artefacts which the Sloathes have looted from the System over the years. When they attempt to escape, they are recaptured and injected with Sloathe reproductive fluid, which contains microscopic Sloathe spores. The spores will feed upon each other until there is only one left in the victim’s body, and unless it is fed with regular injections of the fluid, it will begin to eat its victim from the inside out.

As a child, Leetha was terrified by stories of li Shao’s cruelty and evil, and remains in a constant state of readiness should he try anything -- but all he does is take the rescued prisoners to the asteroid fortress of Sere and then kick them off his ship. The Doctor and Benny find that Sere is on the point of total social collapse; the inhabitants know that their System is doomed, and will soon turn upon each other even if the Sloathes don’t manage to destroy them first. Meanwhile, li Shao has found the papers which Leetha lost, and he decides to set off in search of the Eyes himself; he doesn’t really expect to succeed, but he knows that the System is doomed whatever he does and prefers to go out making a grand suicidal gesture. He needs a new ship for his mission, however, and therefore makes a deal with the criminal kingpin Solan, claiming that he intends to use a new ship to run the blockade and reopen trade routes to the outlying Wanderers. By trading on Solan’s reputation, li Shao thus acquires a beautiful new alien ship, which seems to call to him, and which he names the Schirron Dream.

Since the Schirron Dream is the only ship leaving Sere, Leetha has no choice but to book passage; li Shao doesn’t particularly want her aboard, but the Doctor and Benny have demonstrated useful skills, and they convince him to let Leetha accompany them. Solan realises that li Shao is after the Eyes and attempts to stop him from leaving, but the Doctor distracts him with jokes, sleight-of-hand and a song about an elephant, enabling his friends to escape. They return to the Schirron Dream and depart, only to be confronted by a Sloathe fleet which Solan has guided through Sere’s defenses in exchange for his life. At the last moment, the Doctor presses a button on the control panel and the Schirron Dream’s drives suddenly hit maximum thrust; not only do they escape from the Sloathes, but they reach velocities which will enable them to complete their quest within weeks instead of the months which they may not have.

Roz, Chris and their fellow prisoners are suddenly shipped off-world to Reklon, an Ice Wanderer which by a coincidence of geology and atmospherics looks like a huge snowman smoking a pipe and wearing a hat. Shortly after their departure, the remains of Trenkor Lep’s freighter finally crash on Planet X -- and the thing that remains of Lep, having reverted entirely to its base animal instincts, begin to eat everything it encounters, including its fellow Sloathes. Soon it has eaten every single Sloathe within Planet X, but it’s still hungry, and as it begins to shift itself through the tunnels it realises that it can manipulate the energy field surrounding the System. In doing so, it causes Planet X itself to move -- and accelerates the System’s collapse.

Once out in the System properly, Benny is more than a little startled to see that the “planets” are all connected to the Sun by clockwork. The Doctor explains that they’re in a pocket dimension with different physical laws, and that Benny’s mind is trying to apply familiar concepts to sights so alien she can’t perceive them as they really are. He’s also noted that the people of the System seem to be permanently on edge, as if they’re acting for the benefit of some omnipotent observer without realising it, and has come to believe that something lives in the heart of the System, controlling it all. But first there’s a quest to deal with, and the Schirron Dream thus sets down on the desert Wanderer of Prometheus. There, the tension between li Shao and Leetha is about to explode into violence when a bizarre atmospheric condition suddenly causes the entire company to break into a song-and-dance production number. In the somewhat embarrassed aftermath, Leetha reluctantly agrees to let li Shao lead her to the Valley of the Scorpions, where he grew up and where the Promethean Eye is rumoured to be located.

The Doctor and the polymorph Six accompany Leetha and li Shao to the Valley, where they are exposed to an illusory force which nearly drives them mad with terror. Six saves them by using his species’ defensive telepathic sting; this causes them to see their worst nightmares, which shocks them out of the visions they were already experiencing. Leetha is taken aback when she compares her own worst nightmare, the legendary Nathan li Shao, to the reality of the man she’s travelling with. After the Doctor reveals the presence of another illusory trap, Leetha and li Shao locate the Promethean Eye, which nearly overwhelms Leetha with its power before the Doctor quietly takes it out of her hands and wraps it in copper wire. Back on the Schirron Dream, meanwhile, Benny speaks with the pirate Kiru and confirms her growing suspicion that when li Shao first became a pirate, he spread around a lot of false stories about his evil ways in order to secure his reputation.

The Sloathe freighter carrying Roz and Chris is shot down over Reklon by resistance fighters, who identify the prisoners as collaborators and slaughter them alongside the Sloathes. Roz and Chris escape, and rescue a single Sloathe, Sgloomi Po, whom they need to supply them with doses of the fluid they need to stay alive. While seeking shelter, they fall into the clutches of a Snata, a monstrous creature which feeds on fear by slithering down chimneys and telling its victims that they’ve been very naughty boys and girls indeed. Fortunately, Sgloomi escapes and rescues them, and as they head for the Sloathe excavations, Roz and Chris realise that Sgloomi is beginning to mimic their own appearances and thought patterns. As it learns to think for itself, Sgloomi comes to realise that the Sloathes, shape-shifters with little will of their own, became monsters laying the System to waste because that’s what the people of the System expected them to be when they first arrived.

The Schirron Dream arrives on the jungle world of Aneas, where li Shao is nearly sacrificed to a monstrous leviathan which has subverted the pygmies of the forest to its will. Leetha kills the creature, and while li Shao recovers, the others enter the Anean Pyramid only to find that the monster has already removed the Eye from its hiding place and installed it within its own ship… a ship which looks remakably like the Schirron Dream. As the expedition sets off for the water world of Elysium, the Doctor confides in Benny that the sight of the monster confirmed certain suspicions he holds about the nature of the System. Ever since he arrived, he’s had to control an unthinking abhorrence towards everything he’s witnessed, and he fears that the creature legend has renamed the “Schirron” was in fact known to the ancient Time Lords as a Charon.

The expedition arrives at the hiding place of the Elysian Eye, only to find Solan and the Sloathes waiting for them. Solan has known of the existence of the Eyes ever since a group of refugees tried to trade the Elysian Eye to him for safe passage through Sere; he betrayed them and kept the Eye for himself. The Sloathes take Benny, Six and Kiru aboard their flagship, while the others are returned to the Schirron Dream and prepare to take the Eyes back to Planet X. As they depart, however, the Doctor realises that their course will take them past the Sun; they are still being manipulated by the Charon. He has no choice but to inform the stunned Leetha that the legends of the Chosen are nonsense, created by the Charon in order to get someone to bring the Eyes to it; there is really nothing special about Leetha at all. As soon as the Schirron Dream comes within range of the Sun, the Charon seizes control of it and brings it crashing down on the Sun’s surface, just to the left of the smiley face. Solan and the Sekor Dom Sloathe fall under the Charon’s spell and bring the Eyes to it; as they have now served their purpose, the Charon stops Solan’s heart and drops a ten tonne weight on the Sekor Dom Sloathe.

Aboard the Sloathe flagship, Benny is reunited with Chris and Roz, and learns that with the help of Sgloomi Po they have been converting the Sloathes into rational, thinking creatures. Six is revealed to be a Sloathe, who fell into the company of the polymorphs some time ago and also learned how to think for hirself. Most of the Sloathes come over to their side and help to take over the ship, but at that point Planet X arrives and the eating thing which used to be Trenkor Lep begins to slaughter the fleet. Roz convinces the others to crash the flagship onto the planet and recover the TARDIS, which by now has had weeks in which to repair itself. The eating thing pursues them to the TARDIS, and as they huddle within, Six realises that the TARDIS is a living entity and deduces how he can stop the thing outside. Despite Benny’s objections, Six opens the doors, allows the eating thing to attack him, and stings the TARDIS. The organic component of the TARDIS experiences its worst memories and strikes back with all of the power at its disposal, oblitering Six and the eating thing completely.

The occupants of the Schirron Dream recover from the crash, and the Doctor impatiently ushers them towards the Sun’s interior. Leetha, however, finally realises that he’s been manipulating them all along, and demands an explanation. He is forced to admit that the System was created by one of his people’s ancient enemies, the last of the Charon. Long ago, the Time Lords erased the Charon from the timeline for fear that the people of the Universe could not co-exist alongside them; the people of the System, however, have proven that they can do so, by reinterpreting the horrific images of the System as a series of bad jokes. Somehow this one Charon survived the retroactive extinction of its kind, and although the Doctor doesn’t want to kill it, he may have no choice. The Eyes are in fact extensions into the real Universe through which the Charon draws its power, and they are required to trigger its rebirth cycle. The Charon will be renewed and survive for millions of years, but the current System and everything within will be destroyed. The Doctor leads the others into the orrery room in the centre of the Sun, where he holds off the Charon while the others remove the Eyes from their positions. The Charon strikes at the Doctor with all the power of a sun, but beneath each of the Doctor’s bodies is yet another body, until finally the Doctor’s true form is revealed and he asks the Charon what it really wants. Alone for millions of years, all it wants now is death, and the Doctor sadly grants its wish.

Meanwhile, li Shao tries to remove the last of the Eyes from its position knowing this will mean his death, but Leetha -- acting truly nobly for the first time in her life -- steps into his place, and when he tries to stop her the power of the Eye floods through them both. They survive exposure to the eruption of power, and as the orrery room begins to collapse around them, they take the recovering Doctor back to the Schirron Dream. The System finally crushes in upon itself -- and is turned inside out. The Doctor hadn’t just been manipulating the travellers in order to get to the Charon; they’ve grown from their experiences, and when li Shao and Leetha removed the last Eye the power flooding through them was reshaped by their unconscious thoughts. As a result, the System has been reformed as an actual planetary system; Planet X becomes a life-sustaining moon orbiting a new planet, which itself orbits the sun which had always provided the Eyes with power. The Doctor is reunited with Benny, Roz and Chris, and with his help, Sgloomi Po is able to provide an antidote which destroys the Sloathe spores within their bodies. The Doctor and his companions depart, leaving the survivors of the System to a new life on their new planet.