The beautiful Arielle Markhof travels to the planet Yquatine, the cultural centre of the Minerva system, to begin her studies. As a teenager she was shy and awkward, until her image-conscious mother pressured her into getting cosmetic surgery; as a result, she has become interested in how appearance affects perception, behaviour and social trends. While acclimatising to her new surroundings, she has an unpleasant encounter with a party of Anthaurks, a reptilian species which once tried to conquer the Minerva system after being driven from their homeworld by the Daleks. Senator Zendaak punishes his subordinate for the incident by giving Arielle his invitation to the Treaty Day celebrations at the Marquis’ palace, and thus Arielle meets the Marquis of Yquatine and President of the Minerva System, Stefan Vargeld. By the end of the evening, they have fallen in love. But within a year it has all fallen apart; the Anthaurk have begun attacking trade routes, the Senate has been forced to impose sanctions on New Anthaur, and it seems that the centenary of Treaty Day will be marked by a return to war. Arielle has gone to the moon of Muath, ordering Vargeld not to try to contact her, but he is desperate to settle things before war breaks out, and secretly leaves his world to try to speak with her one more time. But as his ship enters orbit, Yquatine is suddenly surrounded by black alien ships, one of which strikes Vargeld’s shuttle a glancing blow and sends him spinning out of control towards the sun...
Compassion has transformed into the first generation of humanoid TARDISes, and is being hunted by the Time Lords. The Doctor intends to fit Compassion with a Randomiser, but she refuses, confident that she can evade the Time Lords on her own. The Doctor therefore requests that she travel to Yquatine, where they will be able to lose themselves in the crowd of species attending Treaty Day... and where he can purchase a Randomiser in secret from a black-market temporal technology dealer. Before Compassion realizes what he is doing he has installed the Randomiser in her control room -- but to his shock the installation causes her great pain, and in a fit of rage and agony, she expels him from herself and flees. Horrified by the unexpected results, and realizing that Compassion may never trust him again, the Doctor and Fitz split up to search the city for her. The Doctor is unable to find her, and eventually returns to Lombardo’s shop, uncertain how to make things right -- just as the alien ships arrive in orbit and bombard the city with what appear to be gas bombs. The Doctor and Lombardo retreat into the sewers as the air fills with choking black smoke and acid pelts down from the sky. They manage to get to the spaceport, steal an unattended freighter and pilot it to safety, but passage through the gas clouds causes irreparable damage and they are forced to abandon ship in orbit. The atmosphere of Yquatine is becoming toxic and corrosive, and within hours there will be nothing left alive on the planet.
Compassion locates Fitz just as the bombardment starts, and shelters him in her console room -- where she shuts off the air supply and orders him to remove the Randomiser. It is already growing into her, however, and when he tries to tear it free Compassion lurches over a month back in time. Furious and frightened by what she has nearly done to Fitz, she expels him and goes to Beatrix, the industrial centre of the system, to hire a black-market cybersurgeon to remove the Randomiser from her. It continues to embed itself in her, however, and when Petersen attempts to remove it she goes into spasm again, accidentally killing him. Reluctantly accepting that the Randomiser cannot be removed, and upset that she has inadvertently caused a man’s death, Compassion decides to give herself a project to test the limits of her powers. Resisting the pull of the Randomiser, she travels to New Anthaur and uses her chameleon circuit to disguise herself as an Anthaurk. The Senate will soon pass a law forcing the Anthaurk to give up their sacred lands to alleviate the system’s overpopulation problem, thus giving the Grand Gynarch the excuse she needs to declare war after biding her time under a humiliating treaty for nearly a century. Posing as a dissident, Compassion tries to speak sense to the Gynarch, but she is denounced as a traitor and is taken away to be tortured. She has no choice but to dematerialize to escape -- and finds that the Randomiser has now fully incorporated itself into her navigational system. She is lost in time and space, unable to return for the Doctor and Fitz...
The Doctor and Lombardo are picked up by an Anthaurk ship and are taken to Aloysius Station along with the other fugitives from Yquatine. The Doctor brazens his way into an emergency Senate meeting, which is being chaired by Senator Zendaak in the absence of President Vargeld -- angering many other senators, who believe that the Anthaurk are responsible for the attack. Zendaak insists that the Anthaurk “battle fleet” which was on its way to Yquatine at the time of the attack was in fact going to negotiate a new treaty. By now, Yquatine is completely shrouded in corrosive gas, and there is no sign of the black ships. Vargeld is located and returned to the station for treatment, but while disoriented by shock and medication he sets off for Muath again, single-mindedly determined to rescue Arielle. The Doctor accompanies him in the hope of learning the truth, and Vargeld is too preoccupied to question his presence. But Muath is also shrouded in the gas, and although Vargeld manages to land, it is all too clear that he will never see Arielle again. As he grieves for her death, the Doctor notes that the atmosphere around the ship is changing, forming a bubble of air which only he can breathe. He accepts the invitation and steps out of the ship -- but the clouds of gas, apparently controlled by a sentient will, rush forward and attack him. Vargeld dons a spacesuit, pulls the Doctor back into the ship, and returns to Aloysius Station with the comatose Doctor.
Fitz is trapped over a month in the past, with no way to escape Yquatine. If he warns the authorities of the attack to come, he will create a temporal paradox -- and he knows all too well what that sort of thing leads to. He manages to land a bartending job and saves his earnings for a ticket off-world, trying not to consider that he’ll be abandoning his new friends to their deaths. One night, Arielle walks into the bar, trying to get away from the clinging Vargeld and the unwanted fame brought on by their relationship. After chatting to Fitz, she returns to Vargeld and demands that he give her some space -- but he responds by proposing to her, and when she rejects him and tries to leave he becomes violent. Angry and frightened, she storms out and asks Fitz to help her leave Yquatine without being noticed. He thus collects her belongings from the University and arranges to buy tickets off-world. It seems they have both escaped -- but as the ship flies through space, it passes through a particle cloud which has just recently entered the system, and Arielle is the unlucky one who first encounters the spores burrowing through the hull. To Fitz’s shock, Arielle falls into a coma for no apparent reason -- and he is then arrested by Presidential service agents and taken back to Yquatine to explain himself. Arielle apparently recovers, but seems oddly distant, and tells Vargeld that she is going to Muath to continue her studies -- and that he is not to follow her. Desperate to make amends for his earlier behaviour, he agrees. But in the meantime, Fitz will remain in the Yendip Internment Centre until he explains to Vargeld how he came to be with Arielle, what passed between them, and why he has no valid identification papers to prove his citizenship.
Soon after returning to Aloysius Station, the Doctor awakens, locks himself in a quarantine bay and expels the gas creature from his respiratory bypass system. He has communicated with it telepathically, and has learned that the gas is a gestalt entity -- the Omnethoth, a sentient weapon created by a long-extinct alien race. The activation of this colonisation cloud was nothing more than a tragic accident. The Omnethoth transforms into its acidic liquid form and tries to kill the Doctor, but Zendaak saves his life, apparently out of gratitude for proving that the Anthaurk are not responsible for the destruction of Yquatine. The Doctor now intends to telepathically programme the remaining Omnethoth into a new, benevolent configuration, but to his dismay, only their destruction will satisfy the grief-stricken Vargeld. The President orders the system’s fleet to bombard Yquatine, but the attack fails and most of the fleet is wiped out. Once again the Doctor tries to convince the Senate to seek a peaceful solution, but he is too late; the Omnethoth cloud in quarantine has been analysed, and it has been determined that ionisation can disrupt the electrical field that holds the cloud together, thus destroying it. Vargeld thus sends his surviving ships to ionise the atmosphere of Yquatine, knowing full well that an electrical field of such size will kill the attackers as well.
Fitz has spent the last month in prison, steadily slipping into despair as Treaty Day draws closer. It seems to be a stroke of good luck when a mining company seeking cheap labour hires prisoners for construction work on Muath -- but none of his fellow prisoners are willing to risk their parole by trying to escape. Treaty Day rolls around again at last, and only hours before the invasion, Fitz spots a lone space-suited figure some distance away on the surface of Muath. He and a fellow prisoner, Sorswo, are sent to investigate -- and find that the figure is Arielle, who is standing by a vast black organic structure seemingly growing out of the lunar surface. Arielle kills Sorswo and removes her helmet, revealing that she has been possessed by the Omnethoth, but before she can pass the infection on to Fitz, Compassion arrives and saves him -- having finally located his biodata trace after years of wandering lost in the Vortex. Before Compassion can stop her, however, Arielle activates the black structure -- a teleport carrier beacon which summons the Omnethoth colonisation capsules from all throughout the galaxy. The fall of Yquatine has begun again.
Zendaak, apparently grateful that the Doctor has proven the Anthaurk are not responsible for the death of Yquatine, contacts the Grand Gynarch and convinces her to withdraw her ships from the ionisation fleet. He also offers to take the Doctor to Yquatine in a stealth craft, to reprogramme the Omnethoth before they are destroyed. The Doctor agrees, but is suspicious of his motives -- and with good cause. Zendaak in fact intends to capture an Omnethoth cloud and reprogramme it to serve the Anthaurk war effort -- and while the system fleet is in disarray following the ionisation of Yquatine, the surviving Anthaurk ships have orders to attack and capture Aloysius Station. The stealth ship evades the cordon around Yquatine and enters its atmosphere, but they are too late -- the ionisation has already begun, and the panic-stricken gestalt ignores the Doctor’s attempts to contact it. The Anthaurk ship is caught in the ionisation field before it can escape and suffers a catastrophic power failure, and the Omnethoth eats through the ship’s hull, dissolves Zendaak and the ship’s crew, and attacks the Doctor...
As the fall of Yquatine begins, the Omnethoth withdraw their influence from Arielle, and Compassion takes Arielle and Fitz within herself as the Omnethoth begin to bombard Muath. Compassion survives the acid attack unscathed, steals a shuttle and escapes -- but even she cannot save Arielle, whose cells have been ravaged by the Omnethoth as they grew their teleport unit within her. Fitz is forced to watch helplessly as Arielle dies, her desiccated body disintegrating to nothing. Compassion pilots the shuttle to Aloysius, and arrives just as the ionisation of Yquatine is completed -- and the Anthaurk attack. Vargeld, still grieving for the loss of Arielle and his homeworld, is infuriated by the Anthaurk’s opportunism and flatly refusses to surrender, although his forces are heavily outnumbered and the station is full of civilian refugees. In the ensuring chaos, Compassion locates Lombardo, takes him within herself and demands that he remove the Randomiser -- but he is only a salesman and is unable to do so. She realizes that she is about to kill him out of fury -- but she is the first of a new species, and this is not how she wants to start her life. Instead, she releases Lombardo, and then locates Vargeld and uses her chameleon circuit to disguise herself as Arielle. While Vargeld is off guard, she takes him inside, disguises herself as him, and surrenders, ending the battle.
The triumphant Grand Gynarch summons the surviving members of the Minerva Senate as witnesses, and orders the being she believes to be President Vargeld to sign a new treaty giving New Anthaur control over the system’s trade, taxation and economy. To her shock, he refuses to do so; even if he were to sign such a treaty under duress, the other planets would never accept it. Whether he signs the treaty or not, there will be war, and the Anthaurk will be defeated. To the Grand Gynarch’s disgust, the Inner Circle recognizes the truth of what he says, and they agree to negotiate a true and lasting peace instead. The Grand Gynarch will have no part of this, and she allows her daughter to grant her an honourable death and take her place as the new Grand Gynarch. The Anthaurk release their prisoners, and Compassion then releases Vargeld -- who must now deal with the fact that the people of the system regard him as a hero who averted a war, when in truth his stubborn refusal to surrender nearly plunged them all into one.
An Omnethoth capsule suddenly arrives outside the station -- but instead of attacking, it docks peacefully and releases dozens of beautiful, glowing, cloud-like beings... and the Doctor. Realizing that they were doomed, and erroneously believing the Doctor to be one of their creators, the Omnethoth allowed him to reprogramme them to save their lives. But to the Doctor’s horror, Vargeld nevertheless orders his men to open fire, destroying the new, peaceful Omnethoth forever. Furious, the Doctor departs with Compassion and Fitz, leaving the people of the Minerva system to recover from the disaster on their own. Compassion is still angry with the Doctor for what he has done to her, but accepts that he believed he was acting for her own good, and that if she hadn’t run away he would have been able to help her incorporate the Randomiser into herself properly. It is now a part of her, and nobody -- not the Time Lords, not Compassion herself -- can predict where they will end up next.