In pursuit of the Timewyrm, the TARDIS brings the Doctor and Ace to the planet Kirith, billions of years in the future. A young man named Raphael, disturbed by recurring memories of a friend he has never known, has left the shelter of his home to be alone with his thoughts, but a storm is raging outside, and he loses his footing and falls into the sea. The Doctor and Ace rescue him and return him to Kirith town, where his teachers, Tanyel and Miríl, thank them for their help and show them to the seminary’s guest quarters. Tanyel, however, realises that despite the standing orders of the Panjistri, Miríl intends to question the strangers and learn as much as he can from them before, like all other visitors to this planet, they are taken to join the Brotherhood of Kandasi -- and are never heard from again. Meanwhile, the Doctor finds himself troubled by odd flashbacks to his second incarnation, particularly a memory from just after his first regeneration, of a brief meeting with an innocent young girl in an alien marketplace.
The next day, while Ace visits Raphael to see how he’s doing, the Doctor visits Miríl to learn more about the Kirithon. Some centuries ago, a race called the Panjistri landed on Kirith and uplifted the savage natives into a civilisation of peace and enlightenment -- or so they claim. In fact, the Doctor notes several inconsistencies in the official history, and when pressed, Miríl realises that he can’t remember any details about his own childhood. According to the Panjistri, Kirith was once home to another species which destroyed itself in a nuclear war, but when Miríl shows the Doctor the ancient ruins, the Doctor finds that they are mere centuries old and show no signs of radioactive fallout. For some reason, the Panjistri have consistently lied to their charges -- but for what reason? As the Doctor ponders his discoveries, his every move is being observed by the Grand Matriarch of the Panjistri, who believes his arrival signifies an end to the centuries of waiting she has endured. Her genetically engineered Companion, Fetch, becomes concerned when his beloved mistress’ entire personality seems to change; as the Omega Point approaches, she is becoming colder and more obsessive, and she insists that Ace be brought to her immediately…
Raphael tells his story to Lord Procurator Huldah, who orders him to avoid the strangers and not to mention his peculiar memories to anyone else. As soon as Raphael departs, Huldah contacts the Panjistri, claiming that he has found another candidate for the Brotherhood. Raphael’s friend Revna also advises him to avoid the strangers, as they will only lead him into trouble, but Raphael is nevertheless drawn to Ace’s spirit and sense of adventure, and can’t see the harm in talking with her. He eventually tells her about his memories of a friend named Darien who seems never to have existed, and Ace decides to learn the truth. She convinces him to break into the Harbours where the Panjistri dock on the mainland after crossing from their island home of Kandasi -- but Revna, who has secretly been in love with Raphael for hears, has overheard their entire conversation. Jealous, she calls Huldah to warn him that Ace is leading Raphael into danger.
Ace uses her nitro-nine to break into the Harbours, where she and Raphael find a laboratory in which the Panjistri have been conducting genetic experiments -- and have bred a Homunculus full of pain and rage. The Panjistri Reptu confronts them, and claims that the Homunculus will be the salvation of them all, but he refuses to explain further and sets his Companions on them when they try to flee. Ace gives Raphael her rucksack, telling him to warn the Doctor while she leads the pursuing Companions away from him towards the poisonous Darkfell. Raphael gets back to the city and tells his story to Revna, but she does not believe him, and when she warns him to stay away from Ace he realises that it was she who betrayed them. Furious, he storms out on her, and, realising that he will never love her, Revna informs Huldah that Raphael has returned and is seeking the Doctor. Raphael finds the Doctor and Miríl in the seminary and tells them what has happened, but before they can do anything they are captured by the Companions.
Ace loses her pursuers in the Darkfell, where she is contacted by a community of genetically mutilated Kirithon called the Unlike. These are the rejects of the Panjistri’s experiments; their leader, Arun, used to serve the Panjistri until she learned the extent of their deceit and corruption, at which point she became a subject of the experiments she had aided. Arun informs Ace that the miracle food zavát which has eliminated hunger on Kirith is in fact the processed remains of the Kirithons’ own dead -- and that consumption of it lowers the mind’s resistance to telepathic control, enabling the Panjistri to erase the Kirithon’s memories of those who have been taken as subjects for their experiments. Arun learns that the Doctor has been captured and taken to the Harbours, and agrees to help Ace rescue him if Ace in turn promises that the Doctor will help to reclaim the Darkfell, which was poisoned by the Panjistri in an attempt to wipe out the Unlike.
The Doctor, Raphael and Miríl are taken to the Harbours, where Raphael attacks Reptu in anger; he is easily knocked aside, but this still marks the first time a Kirithon has shown aggression towards a Panjistri. The Doctor is taken to Kandasi, where he is abandoned on a hillside and left to make his own way towards the Panjistri’s home, the Skete. The Grand Matriarch and Fetch observe his progress and place obstacles in his path to test him, but the Doctor uses his wits to avoid their traps -- and when he is attacked by violent clones of Ace, Miríl and Raphael, he refuses to give in to his aggressive impulses and kill them. The disappointed Grand Matriarch disposes of the clones, allowing the Doctor to live until the time comes for him to repay her for five thousand years of suffering. Meanwhile, as the Doctor ponders what the Panjistri could do over centuries if they can grow a clone of Ace in just a few days, he experiences a vision of his second incarnation -- a representation of his own buried memories, which are reaching out to his conscious mind through the TARDIS telepathic circuits. The Second Doctor has a reminder for his future self -- a memory of his encounter with young Lilith in the alien marketplace, and of what he unwittingly did to her…
Raphael finds some nitro-nine canisters in Ace’s rucksack, and uses them to blow open the cell door. In the ensuing confusion he and Miríl are reunited with Ace and the Unlike, and tell them that the Doctor has already been taken to Kandasi; they must find some way of crossing to the island without alerting the Panjistri. Before leaving the Harbours, Arun tries to destroy the Homunculus, but Raphael protests, insisting that it cannot help what the Panjistri have created it to be. As they argue, the Homunculus breaks free of its restraints, and to his shame, Raphael is forced to kill it to save Ace’s life. Ace and her friends return to the seminary, where Tanyel refuses to believe their claims about the Panjistri -- until one of the Unlike presents himself to her and she recognises Kraz, her lover, whose existence she had forgotten. Realising that everything they have said is true, Tanyel organises the teachers into a resistance cell and helps Ace to access the computers which control the city’s essential services. Ace shuts them all down, depriving the city of power and food -- and as the citizens march upon Huldah’s office to demand an explanation, the lack of zavát causes the memories of their lost loved ones to return. As Huldah struggles to deal with the unprecedented situation, Revna deliberately withholds vital information from him to make it appear that he cannot handle his duties. The Panjistri are thus forced to quell the rebellion themselves, and Ace, Raphael, Miríl and Arun are able to steal one of their transports in the confusion and cross to Kandasi unnoticed. The Panjistri put down the uprising with a brutal display of force, reinstall the computer systems, kill Huldah for his incompetence and promote Revna in his place. Tanyel, Kraz and the surviving rebels flee into the Darkfell to carry on the fight.
Ace and her friends are attacked by a genetically augmented sea monster on their way to Kandasi, and to Raphael’s horror Miríl is swept overboard and killed. The survivors reach Kandasi and are reunited with the Doctor, but when they finally reach the Skete they find the village to be deserted. In the middle of the village is a large, empty hangar, which the Doctor identifies as the terminal of a powerful transmat unit -- and when activated, it transports them all to the planet’s supposed moon, in fact a space station where the Panjistri are conducting the greatest experiment of them all. The Kirithon did not evolve as natives of Kirith, but were created here, in the laboratories of the Panjistri. Before the Doctor and his friends can confront the Panjistri, however, the station attempts to eject them into space, and in the confusion Ace is separated from the others. Reptu rescues the others, but will not reunite them with Ace, who has been taken to the Grand Matriarch to fulfill her role in the Panjistri’s grand design -- and die in order to save the Universe.
For millennia, the Panjistri have collected specimens from all the species of the Universe, and have distilled them into one physically and mentally perfect race -- and from this species they have further selected the best and brightest, and combined them into a single gestalt organism which is now near completion. The Homunculus was created to supply the gestalt with the rage and aggression which had been bred out of the Kirithon, but now that it is no more, Ace will have to take its place -- and once she is absorbed into the gestalt, it will reach the Omega Point of total experience, and become a god with the power to avert the oncoming Big Crunch and prevent the end of the Universe. But as the Doctor knows, everything must pass on eventually to make way for something new, and the Universe is no exception -- and in any case the experiment is already doomed, thanks to his own unthinking actions in the past. When he last fought the Timewyrm he left it in a weakened state, in which it could be easily defeated -- and it thus broke the laws of Time and travelled into the Doctor’s past, before their “first” meeting, to shelter in his mind while he was still disoriented by his first regeneration. Without realising what he was doing, the Second Doctor passed on the infection to the innocent young telepath Lilith -- who has since grown up to become the Grand Matriarch of the Panjistri. Once the God Machine is complete, the Timewyrm will achieve total control over all time and space…
Reptu doesn’t believe the Doctor’s claims until Kandasi suddenly shuts itself down -- the Grand Matriarch no longer requires the Panjistri’s services. As the panic-stricken Panjistri struggle to maintain the failing systems, Raphael is lured away by a distant fluting sound which reminds him of his friend Darien. Fetch arrives in a state of shock; his beloved mistress has dismissed him from her service and sealed herself and Ace behind a force field in her quarters, where she is torturing Ace to break down her resistance before adding her to the gestalt. The Doctor and Fetch spacewalk around the exterior of Kandasi and break into the Matriarch’s quarters, but they are unable to resist her telekinetic powers, and she callously kills Fetch for his betrayal and forces the Doctor to watch as she prepares to add Ace to the gestalt. But she has left it too late -- for the gestalt has summoned Raphael to itself, and his experiences with Ace have given him the qualities it requires to reach Omega Point. Raphael gives himself up to the gestalt, which achieves apotheosis. As the Doctor and Ace watch, the new God Machine expels the Timewyrm from the Matriarch’s body and regresses her to her youth, allowing her to die as the innocent she was before she met the Doctor.
The God Machine banishes the Panjistri from Kandasi and destroys the station; from now on they will be forced to live alongside the Kirithon and use their knowledge to atone for the crimes they have committed against their creations. The God Machine then sets off to explore what’s left of the Universe, and the Doctor and Ace depart, satisfied that the Universe’s last days are in good hands. But as they go, they see that the time path indicator is still active, and too late, Ace recalls Raphael’s horror when he was forced to kill the Homunculus. He did not kill the Timewyrm, merely banished it -- and it’s still out there somewhere, waiting to strike again.
Source: Cameron Dixon