In the year 1967, somebody called the “Revolution Man” is using some sort of alien technology to carve anarchist graffiti on the landmarks of the world. The Doctor decides that Fitz is too close to the situation to understand the danger, and takes Sam to investigate without telling Fitz what’s going on. Sam, who has always admired the writings of anarchist Jean-Pierre Rex, suggests using him as a contact, but when they meet him at a cafe to discuss the Revolution, Sam realizes that Rex’s ideals have no real organisation behind them and is disgusted when he hits on her. The Doctor asks him about the Revolution Man, but Rex decides he must be an agent of the Establishment and refuses to tell him anything.
Fitz, bored, tries to pick up a waitress named Maddie who works at the cafe. She already has a boyfriend, a singer named Ed Hill, but she likes Fitz and agrees to let him walk her home. Trying to impress her, he claims to be part of a scientific expedition, and, hoping he can help, she tells him about a drug called Om-Tsor which Ed brought from a pilgrimage to Nepal. While taking it with him she had a vision of flying above the Himalayas, but when she innocently touched a passing train she crushed it -- and the next day she heard on a news report that a train was derailed in that same area, killing all aboard. Fitz asks her for a sample of the drug for analysis, but Ed, suspicious, refuses to let her take any. Nevertheless, desperate to know whether she really did kill all those people, she agrees to sneak Fitz into the house while Ed’s band, Kathmandu, is playing a gig at a nearby stadium. Ed has removed most of his stash, and Fitz can only get a couple of flakes -- and while he is occupied, a Chinese man breaks into Ed’s house. Fitz frightens him off, but not before Maddie has been shot.
Policemen at a student demonstration in Rome are killed when their own guns are turned on them by an invisible force. The Doctor and Sam witness the incident on a news report and Sam goes to Rome to investigate, only to be turned over to the authorities by Rex, who has also gone to Rome and thinks she’s following him. In jail, Sam meets an anarchist named Pippa, who clearly hasn’t thought about Rex’s ideas and is simply parroting them; for the first time, Sam realizes how terribly dangerous a good idea can be in the hands of a stupid person. The Doctor bails Sam out, and she is then questioned by both the Italian and British authorities, who believe that the incident was caused by an unknown foreign power which has acquired some new secret weapon. The Revolution Man attacks the British Embassy, and Sam watches as an “R” in a circle is carved into the embassy by no apparent earthly means -- and as an innocent young woman is crushed by the falling rubble.
Sam is released and returns to England, where the Doctor has saved Maddie’s life and taken her to hospital. Fitz goes to the stadium where Ed’s band is playing, to tell him about Maddie, but in the middle of the set, the entire roof suddenly crumbles away and an invisible force plucks Ed up out of the stadium. The panicking audience members are trampled and crushed by the falling rubble. Fitz returns to the TARDIS, where the Doctor has analysed his samples of Om-Tsor and found it to be Rubasdpofiaew, a telekinetic drug from Tau Ceti Minor which has somehow found its way to Earth and into the wrong hands. Fitz, unable to handle the situation, decides to remain and nurse Maddie back to health while the Doctor and Sam take the TARDIS into the Vortex to seek out the next major use of Om-Tsor.
The TARDIS takes the Doctor and Sam to an outdoor concert in 1968, where the Brothers Sunshine -- former members of Ed’s band -- end their set with the clouds themselves moving about to form the symbol of the Revolution Man. The Doctor gets nowhere when he tries to question them, however, as they assume he is an agent of the Establishment. Sam gets further when she is reunited with Pippa, her cellmate from Rome, who is now a member of the Total Liberation Brigade; the TLB has some link to the Revolution Man, and Sam convinces Pippa that she wants to join. The TLB’s methods, however, are slapdash and inconclusive, and one of them gets himself arrested when their attempt to spray-paint anarchist slogans on the American Embassy nearly gets them all shot by security guards. Sam calls the Doctor and convinces him to bail out the unfortunate anarchist to convince the TLB he’s on their side, but Pippa becomes convinced that she and the Doctor are undercover cops and tries to stab the Doctor when he arrives at the TLB safe house. The others restrain her, and agree to let him meet the Revolution Man in person.
Over the past several months the international situation has deteriorated, as the Revolution Man continues to carve his graffiti and the frightened superpowers mobilise for war against an unknown enemy. Maddie, meanwhile, has become obsessed with learning the truth about Om-Tsor. Fitz accompanies her to Nepal, where they ask around for directions and eventually find their way to the village of Ghumding, where Ed first found Om-Tsor and brought it back to the Western world. There, a monk who calls himself “King George” tells them that the monks of his valley used Om-Tsor, “miracle flower”, to create a warm, sheltered paradise in the hidden heights of the Himalayas. When the Chinese invaded Tibet and drove them out, the monks burned all of the plants to prevent it from falling into the wrong hands; but now, thanks to Ed, the last supplies of Om-Tsor are being used by the wrong people, and could bring about the end of the world.
Fitz decides to use his TARDIS recall card to summon the Doctor, but before he can do so Chinese soldiers arrive in the village, having heard that two British tourists are looking for Om-Tsor in Ghumding. Maddie manages to hide with the recall card while the Chinese take Fitz and King George across the border to Tibet. King George is forced to guide them to the valley of Om-Tsor, but secretly takes some of the drug himself and uses it to save Fitz’s life and force the helicopter to crash. Fitz, finding himself stranded in a distant Himalayan valley, searches the gardens of the ruined monastery and manages to locate a few flakes of Om-Tsor -- but then a squad of Chinese soldiers led by the psychotic Jin-Ming arrives and captures him. Fitz takes the Om-Tsor out of desperation, but Jin-Ming works out what he’s doing and takes some himself. Their telekinetic battle causes weather disruptions and tsunami to wash over most of Southeast Asia, and in the end Fitz remains a prisoner. Jin-Ming sends him to a collective for “political education” and takes the rest of the Om-Tsor remaining in the valley...
The TLB introduce the Doctor and Sam to the Revolution Man, who is revealed to be Jean-Pierre Rex -- or so it seems at first. Rex takes the Doctor and Sam out into the back garden and admits that he was the original Revolution Man, until he accidentally killed the young woman in Rome and realized he wasn’t responsible enough to use Om-Tsor as a weapon of anarchy. Someone else has taken his place, and Rex now uses the drug only to observe -- and this house is where he gets his supplies. The Doctor and Sam discover that the TLB have fled while they were speaking to Rex. The Doctor receives a signal from the recall card, and while Sam searches the house for clues the Doctor goes to Ghumding and rescues Maddie. The Revolution Man then kills Rex for speaking with Sam, and attempts to telekinetically crush her to death; fortunately, the Doctor returns just in time to save her. As she recovers inside the TARDIS, the Doctor tells Maddie that he can’t possibly track down Fitz, a single person, in a country the size of China. And then the cloister bell begins to toll; the disruptions in Southeast Asia and the continued activity of the Revolution Man have resulted in a world-wide military buildup as each superpower suspects the others of using a secret weapon against them. On 18 May 1969, the world will come to an end.
Maddie asks to be returned home to Ramsgate, promising to contact the Doctor should she learn anything significant. While attending the funeral of an old friend who died of a drug overdose, she meets another old friend, a member of the TLB who takes her to meet their leader. Their new leader is Ed Hill, who accidentally broke his back and killed several people while trying to stage his disappearance. Paralysed and bitter, he has learned how to grow more Om-Tsor from the petals he has remaining, and has become the new Revolution Man. What’s more, while trying to use Om-Tsor to repair the damage to his spine, he has learned how to telekinetically alter people’s neurons and change the way they think. He does this to Maddie, who becomes convinced that Ed is destined to become a god. Now Ed can use her to get to the Doctor and his magic time machine...
Jin-Ming has similarly used Om-Tsor to brainwash Fitz, but the Chinese have lost their supplies while trying to grow more, and must strike a deal with the TLB. Fitz is sent to England to deliver a bomb to the anarchists in exchange for more Om-Tsor, and Ed sends Maddie to meet him and lure the Doctor into Ed’s clutches. Maddie thus contacts the Doctor and informs him about the planned hand-off, but when Fitz sees the Doctor he panics and flees, taking Maddie with him. Ed, furious, attempts to telekinetically crush Fitz to death, but the Doctor arrives just in time to save him. The Doctor tries to take them all back to the TLB headquarters, but Ed’s use of Om-Tsor has destabilised the historical continuum to such an extent that the TARDIS is unable to anchor itself to contemporary Time. It materializes six weeks too late, on 18 May -- the day the world is to end.
Fitz and Sam find the house empty, and Fitz, who is slowly recovering his own personality from beneath Jin-Ming’s brainwashing, remembers too late that Maddie has a gun. Maddie has kidnapped the Doctor and is forcing him to restructure the TARDIS architecture so Ed’s mind can occupy it. Fitz and Sam ask a neighbour about the TLB, and learn that they are all attending Ed’s comeback concert at a nearby stadium -- and hear the radio announcing that nuclear war is only minutes away, if it hasn’t started already. They rush to the stadium, hoping to convince Ed to use his powers to put an end to the war as he has promised his followers he will. Instead, however, he now believes his destiny is to use Om-Tsor and the TARDIS to become a god.
The TARDIS materializes on stage, and Maddie holds the others at gunpoint so Ed can enter, but Fitz manages to get the gun away from her and shoots Ed in the head. The resulting brain damage causes Ed’s powers to spiral out of control, and the Doctor has no choice but to take the gun and finish him off before his link to the TARDIS causes the Eye of Harmony to explode and take out the Earth. He then uses Ed’s remaining Om-Tsor to stop the missiles and prevent the war, but he, Sam and Fitz must retreat to the TARDIS and depart when the police arrive and Maddie hysterically accuses them of murdering Ed. Maddie goes on to found a cult devoted to the worship of Ed as the Second Coming, but without Om-Tsor the cult dwindles away and ends with Maddie’s death of a drug overdose in 1973. Sam, meanwhile, blames Fitz for forcing the Doctor to take a life, and Fitz is forced to acknowledge that he shot Ed and forced the Doctor to finish him off simply because he panicked.