The TARDIS materializes in the woods near Salem Village, Massachusetts. The Doctor intends to dematerialize and hover in the Vortex, giving him a month to conduct repairs on the TARDIS and returning for his companions after only minutes have passed for them, but they manage to convince him that the ship's fast-return switch isn't reliable enough and he reluctantly agrees to conduct repairs on terra firma while his companions live history for a while. They believe the year to be 1591, a year before the infamous witch hunts, but the villagers are still insular and suspicious of Ian and Barbara's relaxed ways. Susan, trying to fit in with the local girls, joins a s ance with four of them, but the game goes terribly wrong when Abigail Williams foresees a dark omen of her future and has a hysterical fit which spreads to the other girls, including Susan. Later, when she's recovered from the incident, Susan tries to speak with Mary Warren to convince her that there was a rational explanation if they can only understand it, but Mary insists that they were possessed by the Devil. John Proctor finds Susan speaking with Mary and casting doubt on her religious beliefs, and threatens to beat the devil out of her; Susan flees in panic, but the damage has been done...

The Doctor pops into town to visit his companions and meets Rebecca Nurse, a kindly old woman who informs him that the year is in fact 1592; not everyone has switched their calendars yet. Meanwhile, Reverend Samuel Parris has noticed his niece Abigail's distress, and she blames it on Susan. Later, she speaks privately with Mary and convinces her that they should enter the forest and conduct black magic rituals, using the Devil's own ceremonies to cleanse themselves of his evil. The Doctor, despite his sympathy towards Rebecca Nurse and her inevitable fate, convinces his companions that they must leave immediately, but despite Ian's attempts to distract the constables, Reverend Parris notices the others fleeing into the forest. Determined to root out their evil at its source he follows them into the forest, only to find his own niece and her friends conducting black magic ceremonies...

The Doctor and his companions escape, and the TARDIS takes them to Bristol in 1954, where it just so happens a production of The Crucible is playing. Susan is horrified when she learns what happened to, and because of, her friends, and refuses to accept the Doctor's insistence that it is impossible to change history. Instead, she uses the TARDIS' fast-return switch to take it back to Salem, hoping to talk some sense into her former friends... but the ship materializes in June, when the witch-hunt fervour is at its height and people have already died. Rebecca Nurse is found not guilty, but when the verdict is read out the girls go into further convul- sions and blame her, and she is re-arrested. John Proctor and his wife are in prison, accused of witchcraft by Mary, and Mary and Parris refuse to listen to Susan's blasphemous attempts to convince them that there's a rational explanation for what's happening. In fact, Susan herself is almost convinced by their certainty, and she's starting to get sick headaches when she tries to argue with them.

The Doctor, realizing he'll never be able to talk Susan out of her attempt to change history until she learns for herself, remains with her in the village. Ian and Barbara, unable to remain in the TARDIS while their friends may be in danger, emerge at night only to encounter a coven of real witches. The coven releases them, ordering them never to speak of what they've seen, and Ian assumes history has been changed until the Doctor explains that the "witches" are also suffering from hysteria. The repressive atmosphere of the Puritan colony has led to human beings' natural emotions and resentments being pushed under the surface, and now they've exploded in several forms; some believe they are possessed and tortured by witches, and some believe they actually are witches.

Mary Williams dreams of being attacked by witches, one of whom has Susan's face, and in her confusion she tells Abigail what happened. Abigail later overhears Parris speaking with Cotton Mather, who has come to oversee the witch trials, and when Mather questions her she pretends to go into a fit and blames Susan and her family. Ian, meanwhile, helps Francis Nurse to write a petition for Rebecca's release to be taken to Governor Phips, and manages to convince foreman Fisk of the jury that he misinterpreted one of her innocent comments û when she referred to another accused prisoner as "one of us" she meant a fellow prisoner, not a fellow witch. Parris accuses Francis of consorting with a known witch, and Ian agrees to accompany Francis to Boston with his petition as quickly as possible.

The Doctor learns of Susan's delirium, and upon learning that she and Mary shared a dream he realizes that Susan's undeveloped telepathy is leaving her open to the hysteria of the townsfolk û and some of it may be feeding back to them, increasing the hysteria. He installs a few mental blocks in her mind and tells Ian that he'll accompany Francis to Boston while Ian and Barbara remain in Salem to protect Susan; they'll escape when the Doctor returns from Boston. But their plans fall apart at the church service on Sunday, when Parris has Rebecca Nurse brought before his congregation and publicly excommunicates her. Susan can't stand it and speaks out against this fresh cruelty, but the townsfolk turn on her and chase her to the river, where they attempt to drown her. Ian saves her but is himself arrested, and Parris takes Susan into his home to ensure she gets a proper religious upbringing. By the time Barbara gets to her, she's been starved of food and worked solidly for a day, and her mental blocks against the townsfolks' hysteria break down and she deliriously accuses Barbara of witchcraft as well. Barbara flees in panic to the TARDIS, but is followed, and the townsfolk prepare to burn the "temple of Satan". Barbara and the Doctor are trapped inside, and the Doctor realizes that rather than present the people of Salem with a magic fireproof box, which would seem to prove their beliefs that the Devil walks among them, he's going to have to dematerialize in the midst of the flames and trust to the fast-return switch to bring him back to rescue Ian and Susan.

The TARDIS doesn't return for another two weeks, however, during which time Ian is beaten, degraded and humiliated in Salem jail, and Susan must bow to the wishes of Parris and uphold her former friends' accusations of witchcraft against innocent people in order to avoid being accused herself. Several "witches" are taken to be hung, including Rebecca Nurse, and while most of the townspeople are at the spectacle, the Doctor and Barbara take advantage of the opportunity to rescue Ian from the jail. For some reason the jailer seems to recognize the Doctor as an emissary from Governor Phips and releases Ian; Ian nearly ruins everything when he tries to help John and Elizabeth Proctor to escape as well, but the stress of the escape causes the pregnant Elizabeth to go into labour, and John sends Ian and the others on ahead, as he doesn't want to slow them down and prevent their escape. They go to Parris' home, where they confront him, Mary, and Abigail. The Doctor points out that the source of the evil began in Parris' own home as proven by Abigail's convulsions, and Susan plays along by pretending to have a fit and accusing Parris of causing it. Mary stands up to Parris and corroborates Susan's accusations, and Parris is forced to let his enemies go under threat of being taken to the gallows with them. Mary remains behind to do what she can to ameliorate the witch hunt, atoning for her sins, and when the hysteria eventually does die down she leaves the town to find a new life elsewhere.

The Doctor tests his newfound confidence at navigation by taking the TARDIS about fifty years into the future, while Ian and Barbara ponder the Doctor's actions; he never told them how the appeal for Rebecca Nurse's release turned out, and according to Barbara's history texts the appeal was rejected when Governor Phips was talked out of it by an unnamed Salem gentleman. Did the Doctor act to preserve the course of history at the cost of Rebecca's life?

Much later, after the events in the Death Zone on his home planet, the Doctor is granted an unexpected bonus: the chance to travel back to Salem and speak with Rebecca Nurse the night before her execution. Presenting himself to the jailer as an emissary from Governor Phips (which explains the jailer's reaction the following day), he temporarily releases Rebecca from the prison and takes her into the future to see how the witch hunts are perceived. Upon understanding that her martyrdom is part of the reason why such hysteria will never happen again - or so the Doctor lets her believe - Rebecca is able to return to Salem and face her execution with quiet dignity.