The TARDIS suffers from an artron energy drain while materializing in the grounds of Norton Silver’s family estate in the English countryside. Silver welcomes the Doctor, believing that he is a historian who has come to solve the mysteries of the Silver family heritage. Silver himself is a hypnotist who works freelance for the Ministry of Defense, training soldiers to resist brainwashing techniques. The Doctor throws himself into his work with the help of a local archivist, Sargent, while Sam spends her time with Silver’s young wife Penelope and Silver’s latest training subject, Captain William Pickering. The Doctor and Sargent, meanwhile, find inconsistencies in the Silver family history and allusions to a secret society which has been in existence for several hundred years. One night in the 13th century, a group of alchemists led by Matthew Siolfor experienced some sort of revelation, but all record of that night has been excised from the family history, apart from scattered allusions to the Devil and to a chapel which doesn’t exist.
The Doctor notes several other oddities on the estate: the proliferation of a strange blue alien flower in the grounds; a repeated gargoyle motif in the architecture; a strange glowing artefact called the Philosopher’s Stone on display in the family library; and a series of paintings of the landmark Lord Meacham’s Clump which were never completed, as the artist committed suicide while working on the last one. While working late at night in the library, the Doctor finds a secret panel containing the last, incomplete, painting. Somebody turns out the lights and attacks him, but flees when Sam arrives; the Doctor and Sam lose the figure in the grounds, but work out that the Doctor was attacked because the figure thought he’d actually discovered a different secret panel. The second secret panel contains a genealogy tracing the descendents of the original alchemists -- and seems to suggest that the Society is still active.
America’s national security advisor is assassinated, and his replacement, Pete Kellerman, requests assurance before he accepts the offer that the so-called Station Nine -- the ninth base of defense in the event of a nuclear war -- does not in fact exist. Dering assures him that there is no such place, but Silver is unconvinced when Kellerman reports to him. In order to force the Americans to reveal the existence of Station Nine, Colonel Anatoli Roskov -- commander of the Nevchenka nuclear base in Krejikstan -- must carry out a dangerous plan. Meanwhile, Silver continues his work with Pickering, and allows Sam to sit in on one such session. When she mentions that Pickering told her he was a liaison officer with NATO, Silver, who had been unaware of that, takes the opportunity to ask him about Station Nine. Unfortunately, he has already conditioned Pickering to resist questioning along such lines. Disappointed, Silver then hypnotises Sam to -- amongst other things -- forget what she’s just seen.
Pickering departs, his training complete, and as soon as he’s gone Silver and his servants turn on the Doctor, Sam and Sargent, taking them prisoner. Silver’s servants Tanner and Allworthy are also descendents of the original alchemists and thus members of the Society, as are Kellerman and Roskov. Sam manages to escape, but the Doctor and Sargent are marched into a secret tracking base beneath Abbots Siolfor to watch the result of Roskov’s actions in Nevchenka. Upon returning from England, Roskov takes his nephews Gregor and Ivan into the tracking room with him, and although his second-in-command Lieutenant Ivigan becomes suspicious he acts too late. Roskov uses CD-ROMs given to him by Silver to run a simulation of a nuclear attack which appears to the technicians in the tracking room to be the real thing. Ivigan and his men are sealed out of the tracking room, while the computers inside print forged launch authorisations.
As a desperate attempt is made to warn the States of the imminent launch, Ivigan and his men try to seize control of the facility and shut down the missiles. Roskov and his men kill the technicians inside the tracking room when they realize that the events they are witnessing are simulated, and Ivigan and his men break in too late; Roskov and his nephews are shot down just as they turn the launch keys. Nevchenka’s missiles are launched at the US mainland, and with only seconds to go, General Howard Kane of the Joint Chiefs has no choice but to reveal the location of Station Nine -- a secret space station armed with missiles of its own, which target the approaching ICBMs and blow them out of the sky. Faced with a possible public relations disaster, President Dering then has no choice but to admit the existence of Station Nine to the world, and to turn it over to the United Nations as an international peacekeeping station -- just as Silver had planned.
Sam frees the Doctor and Sargent, and the Doctor, having finally worked out what drove the artist mad, takes them to Lord Meacham’s Clump. The copse in the clump appears exactly the same from every angle, and this impossible perspective drove the artist mad when he realized the truth. The Doctor, Sam and Sargent push through a psychic fear barrier around the Clump and find that it is in fact a hologram, masking the chapel mentioned in the Silver family records -- and the alien spacecraft which crashed into it in the 13th century. The gargoyles on the estate are based on the features of the ship’s crew, and the alien flowers were expelled from a broken seed pod carried in its cargo.
The Doctor identifies the ship as a Khameirian cruiser, brought down by a missile from a Yogloth slayer; as the crippled ship approached Earth, the life essence of the crew was distilled into the Philosopher’s Stone. The alchemists who witnessed the crash were imbued with the life essence of the ship’s crew, a subconscious influence which has been passed down through the generations. When the TARDIS arrived nearby, the Stone drained its artron energy reserves and the subconscious influence of the Khameirians took control of the alchemists’ descendents. Society members all over the world are now preparing to give the Philosopher’s Stone the energy it requires to reconstitute the Khameirian life forms -- but to do so will require the energy of a nuclear detonation.
Thanks to Society members’ influence, Silver’s estate is chosen as the site of the conference at which control of Station Nine will be handed over to the UN. Canadian colonel Jean-Pierre Tannerie is already on his way to the station to take his place as the new commander. Security forces arrive to secure Silver’s estate, and nearly capture the Doctor and Sam. Fortunately, the Doctor realizes at the last moment that Sargent’s name is derived from S’Argent, or “silver” -- he too is a Society member, and he is leading the security forces to them. The Doctor and Sam ditch Sargent and escape back to London, where they contact Pickering and tell him the truth. Although their story is difficult to swallow, Pickering must admit that the speed at which events are moving is odd, as is the fact that Roskov nearly started a war just after meeting with Silver. As it happens, Pickering has been chosen to represent British interests on Station Nine, and he is about to depart to take up his place.
The Doctor and Sam leave him to his work and return to Abbots Siolfor, but they and the other delegates are captured and held prisoner by the Society members. The Doctor realizes that Silver, disoriented when the Khameirian programme reasserted itself, welcomed him upon his arrival in the belief that the Doctor had come to ease the confusion in his mind. As the alien influence grew, however, he came to realize the Doctor was a threat, which was why he had Sargent infiltrate the Doctor’s group and tried to hide the Society’s geneaology from him. The Doctor attempts to reawaken Silver’s buried sense of self, but fails and is forced to watch as a simulated attack from China tricks Dering into releasing the Station Nine codes to Tannerie. Tannerie shuts off all communication with Earth and re-targets the missiles to strike Abbots Siolfor; the resulting energy release will be absorbed by the Philosopher’s Stone, and the Khameirian will be reborn.
At the last moment, Pickering unexpectedly shoots Tannerie, stops the launch and forces the crew to evacuate. The British government, unwilling to leave their nuclear defense in the hands of NATO, had arranged for Silver to implant post-hypnotic commands in their liaison’s mind to ensure he had no choice but to act under certain circumstances. Without realizing what he was doing, Silver has programmed Pickering to prevent any launch not authorised by the British government. Silver orders the Doctor to take him to Station Nine in the TARDIS, where Pickering holds him off at gunpoint -- until Silver quotes a post-hypnotic code phrase and Sam attacks Pickering, catching him off guard and taking his gun. As Silver prepares to complete the launch, the Doctor manages to distract Sam for a vital moment, but she shoots Pickering before he can get the gun away from her. Knowing that he is dying, he tells Sam to tell him that free will is not an illusion -- and when she does so, this triggers another set of hypnotic commands, turning him into a killing machine who attacks Silver without thought for his own wounds or safety. The Doctor and Sam escape in the TARDIS as Pickering activates Station Nine’s self-destruct system, killing himself and Silver.
With the departure of the TARDIS and the death of Silver, the other Society members return to normal. Since Silver was the direct descendent of Matthew Siolfor, who first accepted the Philosopher’s Stone from the Khameirian, he contained the greatest concentration of its life essence; and since he had no descendents, the Khameirian life force seems to have dispersed forever. But the Doctor and Sam don’t know that Penelope Silver is pregnant...