While the Doctor and Jo are away, taking the Doctor's apparently repaired TARDIS on a test flight, UNIT is called in to investigate the crash of an RAF plane which had reported seeing a UFO. The dead body of the still-living MP Frederick Jackson is found aboard, and autopsy reports indicate that the body is that of the genuine Jackson, although his appendectomy scar seems to have vanished. The Brigadier requires a new scientific advisor to help solve the mystery, and as Liz Shaw is away on a lecture tour, he contacts the RAE and is put in touch with Ian Chesterton and his wife Barbara. Ian soon determines that the crashed aircraft is mildly radioactive, indicating that it has recently been somewhere other than the Earth, but before he can investigate further, the Minister without Portfolio Carswell arrives and demands that the plane be disposed of to prevent radioactive contamination of the countryside. Against orders, Mike Yates removes a fragment of the wreckage for Ian to examine later.

The Magnum Bank is raided by robbers armed with AK-47s, and when Detective Inspector George Boucher and his nephew and partner Rob Thorpe enter the bank without waiting for backup, Thorpe is gunned down by the escaping robbers. Boucher is left to agonise over how to tell his sister about Rob's death, and only feels worse when he is taken off the case due to his personal involvement. The robbers targeted specific safety-deposit boxes owned by the criminal mastermind Victor Magister, who prefers to be known as "the Master", and he orders his criminal lawyer Ross Grant to investigate and teach the perpetrators a lesson. Grant has Joseph Barron question an informant and learns that the raid was apparently planned by the "69 Krew", a Scottish criminal syndicate. He therefore leads a team of heavies to teach the Krew a lesson, but realizes too late that Barron has led him into a trap; the thugs from the Master's gang are all killed, while Grant is taken prisoner and tortured by the Master's accountant, Marianne Kyle.

Barbara, seeking something constructive to do, goes to interview Jackson to determine whether he is the real thing, only to find that he has been murdered. Boucher is assigned to the case, and the Brigadier, unable to fill him on the full details for reasons of security, asks Barbara to help Boucher in case he should find something relevant. Barbara learns that Jackson's replacement is hiring new people to fill positions amongst his staff -- and that the ads were placed a week ago, long before Jackson was killed. Boucher and Barbara research recent missing persons reports, and discover that a number of prominent politicians have recently vanished and then reappeared within a few days -- and that one of them was Carswell, the man who tried to have the suspicious plane destroyed. The Brigadier assigns Lieutenant Beresford to keep Carswell under surveillance, and Beresford soon spots Carswell meeting with Joseph Barron, arranging for more of Kyle's people to be "brought over"; Carswell also meets with a group of men who are later traced to the Royal Navy's submarine base at Faslane.

Ian determines that the radioactive damage to the plane could not have occurred on Earth, which means they need alien technology to analyse it. Since the Doctor is not available, Benton suggests turning to the Master, who is still imprisoned in Aylesbury Grange detention centre. The Master, although amused by the Brigadier's request for help, refuses to assist him unless his freedom is restored, and the frustrated Brigadier returns empty-handed to UNIT HQ. There, Corporals Bell and Osgood have analysed the recording of the downed plane's last transmission, and have heard the chimes of Big Ben in the distance, proving that the transmission was faked. Something else happened to the plane, and the people responsible are familiar enough with UNIT's true agenda to falsify a UFO report to set them on the wrong track. Meanwhile, when forensics reports indicate that Jackson was killed with the same weapon used in the Magnum bank job, Boucher is taken off the case and given compassionate leave. The Brigadier, sympathising with his plight, tells him of the connection to Faslane, and Boucher goes there to investigate on his own time. There, he breaks into the naval yard and discovers that one of the navy's helicopters is the same one used on the bank job. He is spotted and recognized by Kyle, and is chased by ratings who attempt to shoot him rather than arrest him. He flees from the base, but in his haste to get away runs out onto the road, and is struck and killed by a passing motorist. A naval surgeon named Harry Sullivan happens by the accident, and the dying Boucher tells him to get word to Brigadier Lethbridge-Stewart of UNIT.

Kyle sends her agent Voshinin to dispose of the Master, but the Master has already hypnotised the entire prison staff and only remains in the prison while it suits him to do so. He escapes before Voshinin can get to him, but mistakenly assumes that the attempt on his life was made by the 69 Krew and returns to the bank to discuss retaliation with Kyle. By now, Kyle has learned from the dying Grant that the Master is a Time Lord, and after their meeting she and Barron secretly follow the Master to a Rolls Royce which she realizes is his TARDIS. While the Master prepares to meet the leaders of the 69 Krew, Kyle arranges for his TARDIS to be sent to Faslane and then on to the Conclave. Barron, assuming that Kyle only wanted the Master alive for his TARDIS, decides to eliminate him on his own initiative, and takes two attack helicopters to the hotel where the Master is attempting to impose his will on the representatives of the 69 Krew. The Master escapes again, but knows that only Barron and Kyle knew where to find him -- and when he tries to return to his TARDIS he finds that it has been taken beyond the range of his sensors, indicating that it was stolen with technology beyond that of the 20th century.

Kyle abandons Barron to his fate, and the Master tracks him down and tortures him for information, only to learn that Barron believes Kyle and her associates are members of the Russian Mafia who are bringing their own people over to fill prominent positions in Britain. As this is obviously not true, the Master disposes of Barron, and reluctantly turns himself in to UNIT, knowing he will need their assistance. The Brigadier has serious reservations and is fully aware that the Master has an agenda of his own; nevertheless, he reluctantly accepts the Master's help and gives him access to the Doctor's laboratory. There, the Master sets about using the defunct time machines from the Dalek-invasion timeline to detect phase shifts and the operation of time machines in the vicinity. Boucher apparently returns, claiming to have found nothing at Faslane, but he soon slips up and is revealed to be an impostor. Realizing that he has been found out, Boucher takes Barbara as a hostage and flees from UNIT HQ, and to discourage pursuit he kills a homeless woman who resembles Barbara and makes it appear as though she burned to death in a car crash.

Ian is devastated by Barbara's apparent death and nearly commits suicide, but the Master, who still needs his help, talks him down and convinces him to turn his despair into anger for use against his enemies. An autopsy of the woman's body reveals the truth, but the Master intercepts the information and keeps it from Ian in order to keep him focussed on the task in hand. Barbara, meanwhile, is transported to a world which has been devastated by some natural disaster, and finds that its occupants are travelling via a dimensional transference arch linked to what appears to be the TARDIS console. She is interrogated and admits to being only a schoolteacher, but Kyle can't believe that she's nearly been outwitted by mere civilians, and has her sent to the Conclave for more in-depth interrogation. Meanwhile, the Master detects a transference shift in Faslane, and the Brigadier receives a call from Lieutenant Harry Sullivan telling him about Boucher's death. Boucher's body has vanished from the morgue, however, and when Sullivan checks the paperwork he finds that the body was taken by a "Doctor Williams" -- who doesn't exist. Sullivan waits in the morgue and nearly catches Williams trying to remove the paperwork, but when he tries to call in ratings to arrest him, the ratings try to kill Sullivan instead. Sullivan escapes and warns the Brigadier, who now must determine how many people in the base have been compromised.

Using the Dalek time machine, the Master builds a device which will enable three travellers to follow the phase shifts to their source. Ian, Yates and Benton use the device and are transported to a radioactive plain, where they see the prototype NASA shuttle coming in for a landing -- with an unfamiliar flag on its side. When they return to Faslane with their story, the Master soon guesses that they were transported to a parallel timeline. The Brigadier sends to UNIT HQ for the file on the Inferno incident, in which the Doctor travelled to such a timeline, only to find that it has been stolen -- by Corporal Bell, who admits that she has been spying for the duplicates since they kidnapped and threatened to kill her brother. The parallel Earth was all but destroyed by the fallout from the Stahlman Project disaster, but the few survivors -- the leaders of the totalitarian Earth -- were alerted to the existence of parallel Earths by the Doctor's arrival, and they are thus planning to escape from their dead world and replace their counterparts on this Earth.

The Master attempts to transport himself to the parallel Earth and recover his TARDIS, and the Brigadier and Ian are transported along with him while trying to stop him. There, the Master turns himself in to the surprised Kyle, claiming that he has come to help her, and to prove his loyalty he turns in the Brigadier and Ian. However, the Brigadier finds a gun in his cell, along with one of the Master's gloves, indicating that the Master has another agenda in mind. The Master is taken to the home of the Conclave, a moonbase in which the leaders of the world survived the destruction of the Earth; there, he learns that their transference arch is linked to the TARDIS of his own counterpart. In this world, the Master -- still a loyal Time Lord named Koschei -- was stranded on Earth when his TARDIS was destroyed in a battle with an Intelligence which tried to shroud the world in web. The Conclave learned of the TARDIS' abilities due to surveillance records of the Doctor's activities at the Stahlman project, but when Koschei refused to help them evacuate to an alternate Earth, they imprisoned and tortured him for information. Koschei is now on his final incarnation, and is kept alive, in agony, by life-support systems.

The Master claims to have no feeling for his counterpart, and agrees to mass-produce demat boxes for the Conclave. First, however, he claims he must interrogate Barbara -- and once he reaches her cell he helps her to escape and uses the distraction to get to his own TARDIS. He has no intention of helping the Conclave, who must be taught a lesson for torturing his counterpart and attempting to use him as their pawn. Kyle returns to Faslane to warn her compatriots of the Master's treachery, while the Master kills Koschei at the dying Time Lord's request. The Master then takes Barbara to the parallel Earth, where the Brigadier and Ian have escaped; despite his hatred of Boucher, Ian is unable to take his life, but the Master does so, casually revealing to the stunned Ian that Barbara is alive in any case. He then destroys the space-time element and dematerialization circuit from Koschei's TARDIS, thus depriving the Conclave of their transference arch and stranding the remaining Conclave members in this continuum.

Yates and Sullivan manage to convince Faslane's commanding officer, Commodore Bennetts, that his base has been infiltrated by traitors. Bennetts, who believes UNIT to be a covert anti-terrorist squad, agrees to submit his men for screening, and Sullivan soon identifies "Williams" as the CPO of the HMS Redoubt -- a nuclear submarine which has been submerged in an experimental IDPF net for magnetic degaussing, and which will therefore be undetectable if the duplicates manage to escape. The Master materializes aboard the Redoubt to complete his work and destroy the other end of the dimensional link; however, he allows Kyle to escape, amused by her persistence and by the thought of leaving her alone and friendless on an alien world, perhaps to cause trouble for the Doctor some day. His work done, he attempts to evade the Brigadier and return to his TARDIS, but he is captured by Yates, Benton and Sullivan, who have boarded the Redoubt to prevent the duplicates from escaping. Before the Brigadier can impound the Master's TARDIS, he sends it by remote control to the crypt of Devil's End. The Master is then returned to prison, and some time later, the Doctor and Jo return, having discovered to their disappointment that their trip to Peladon was engineered by the Time Lords, and that the Doctor is still exiled to Earth.