Historian Evelyn Smythe is lecturing her students on Tudor history when a man in a silly coat enters the hall with a bleeping electronic device, claiming that the fate of the planet is at stake. She is forced to cut short her lecture before she can discuss the role her own ancestor, John Whiteside-Smith, played in the fall of the Spanish Armada. As her students depart, Evelyn attempts to take the stranger to task, but he discovers that Evelyn herself appears to be the temporal nexus point he is looking for. She doesn't believe his claims, even when he claims to be a doctor himself, and storms off in a huff when he informs her that there was no such person as John Whiteside-Smith. He follows her home, insisting that this "John" may be the anomaly he's looking for, if indeed Evelyn is related to a person who did not exist. Eventually, she agrees to let him see her family historical records in order to get rid of him -- even if she does believe that he's been sent by the faculty to convince her she's gone mad so that she'll retire.

As Evelyn searches for her family records in her cluttered home, the Doctor gets the impression that she's well-liked by her students, even if the faculty isn't that fond of her forthrightness. Eventually she finds the books she's looking for, but to her surprise John Whiteside-Smith isn't listed in the index. She's studied her family history in great detail; John's father was executed by Queen Mary, his mother was one of Elizabeth's household, and John himself was the first distinguished member of the family. She tries to prove her claim by showing the Doctor her family tree, which one of her students had printed out on the computer -- but to her shock, half of the page is blank, and the rest of the type is fading away as she watches. The Doctor has been telling the truth all along; something has gone wrong with Time, and her entire family is being erased from history. Evelyn herself has been suffering from headaches over the past few days and has been forced to take analgesics for the pain -- but the cause of her headaches cannot be cured by pills, and unless the Doctor can do something, Evelyn will cease to have ever existed.

The Doctor's only lead is the mysterious John Whiteside-Smith, and he decides to travel back to the court of Elizabeth to find out more about him. This is an offer which Evelyn cannot pass up, and even though the Doctor has not actually made the offer he is somewhat taken back by her determination to accompany him. After packing up the necessities for the trip -- toothbrush, aspirin, and a tin of cocoa -- she heads back for the TARDIS with him, looking forward to her journey. As far as Evelyn is concerned, Queen Elizabeth was the greatest female leader of history -- much better than Mary, who nearly tore her country apart with her marriage to the Spanish Philip and the burning of Protestants at the stake. Despite herself, she is impressed by the TARDIS interior, but when the Doctor travels back in time he materializes very close to the historical nexus point, and Evelyn finds herself fading in and out of existence. Until the nexus has been stabilised, Time itself is uncertain whether Evelyn should exist. The Doctor builds a device to stablise her, and warns her to remain within three metres of it at all times. He also advises her to remain in the TARDIS while he goes to the court and prepares the way for her; however, she refuses to stay put while history is taking place all about her. Instead, she will go to a traditional English tavern and speak with the locals, to get a feel for life in the sixteenth century. What could possibly go wrong?

Leaf and Crow drag the protesting Evelyn outside -- and release her, convinced that she's come to help and that she was just testing them. She's not the only one who thinks that Elizabeth should be on the throne, although Evelyn has now realized that she's arrived too early for that. They take her to a safe house to meet the Reverend Thomas, admitting that they are Protestants and proud of it -- but since the Heresy Laws were passed in 1554, they risk being burned at the stake for their beliefs. Evelyn warns them that Mary will be a Catholic for life, and wonders what they intend to do about it -- but just as they are about to tell her, the Reverend Thomas arrives and interrupts them. He's heard everything they've said, and is furious that they have nearly revealed everything to a woman they've never met before. He orders them to go out and ensure that Evelyn wasn't followed here, while he questions her to determine whether she's really a spy.

Queen Mary dismisses Sarah and speaks with the Doctor, who senses that she is troubled in mind as well as body. Mary, sensing that there is something different about this Doctor, and admits her fears that she will not survive her pregnancy at the advanced age of 38. If she dies heirless Elizabeth will take the throne, and what will become of her country then? Her only comfort now comes from knowing that England will be cleansed of the Protestant scourge before her death, as those who do not turn from the path of sin will be purified in the flames. She realizes that the Doctor does not approve, but welcomes his viewpoint, as she is surrounded every day by courtiers who seem to have no opinions of their own. The Doctor points out that she stayed true to her own religion during the reign of Edward; why kill people for staying true to their own religion during her reign? When -- or rather, if -- Elizabeth takes the throne, Mary's name will be blackened in the eyes of history. But she cares nothing for that, knowing that when she dies she will be in the arms of the Lord -- and how wrong it is that those of strong faith must suffer for all eternity for placing their faith in a false religion! Nevertheless, she appreciates the Doctor's bravery in challenging her, and invites him to remain while she speaks with the Bishop of Aix, brother of the French ambassador; that way she will be assured of an intelligent presence.

The suspicious Thomas questions Evelyn further, convinced that she is a spy sent to learn the truth about their plot. Fed up, Evelyn insists repeatedly that she is no such thing, and that if he's going to overthrow Mary then he's going to have to trust people. She has a friend called the Doctor who may be able to help him; he knows many people, such as William Cecil, who support Elizabeth. But even if he could help, she knows that no rebellion would succeed; Wyatt tried just that the previous year, but failed when the people of London rose up to protect their queen. How can Thomas expect to put Elizabeth on the throne with only a few plotters behind him? She suggests that he flee the country to safety, but he refuses; he will not save his own skin by abandoning those like Leaf and Crow who have nowhere else to go. Evelyn admires his courage, and assures him that within a few years Elizabeth will take the throne when Mary dies of natural causes. He need not worry about Mary bearing an heir; she cannot have children, and her current condition is a phantom pregnancy. Thomas is quite intrigued by this news...

The Doctor sits in on Mary's audience with Francois de Noallies, Bishop of Aix. He is here to speak about Elizabeth; the Heresy Laws are upsetting the people, and by reconciling with her sister and releasing her from house arrest, Mary can perhaps increase her popularity. But Mary will have none of it, and the Doctor agrees with her that de Noallies is simply trying to curry favour with Elizabeth for the good of his country. It is well known that Anne Boleyn had symapthies for France, and perhaps her daughter would as well, if she were on the throne. The Doctor advises Mary to rest, while he escorts de Noallies to the door -- and tells him in no uncertain terms that he might as well save his energy if he's plotting to put Elizabeth on the throne. de Noailles storms out in a huff, leaving the Doctor to speak with Sarah, who is grateful to have him in attendance. Mary has suffered greatly since she learned she was with child -- but the Doctor knows that she is not, and that telling her so would cause her distress beyond anything he can imagine. Trying to set the matter aside, he asks Sarah to send a messenger out to look for his companion Evelyn.

Leaf and Crow report to Thomas that nobody is watching the house, and Thomas reluctantly decides that she is not a spy after all. Relieved, she gets out her bag to make a nice cup of cocoa, and asks Leaf to fetch the sweeteners from its side pocket while she boils the water to make it safe. The illiterate Leaf hands over her analgesics, and she reads out the warning on the side, pointing out that these are pills for her only and that exceeding the stated dose could prove fatal. She then makes cocoa for Leaf and Crow, telling them that it's a drink from the New World -- and is taken aback to find that neither of them have heard of the New World. History is taking place all around them, and they've no idea! Crow is disgusted by the sweet taste, and, dismissing it as a drink for children, heads back to the pub for some proper ale... but he returns soon afterwards, claiming that a messenger from court had come with an urgent message for Evelyn. Evelyn realizes that the Doctor may have turned up in the court of Queen Mary believing that Elizabeth was on the throne, and rushes out with Leaf to ensure that he is safe.

Queen Mary is terrified of plots against her life, and Evelyn is carrying pills which she claimed could kill... or at least she would be if she hadn't forgotten her bag in Thomas' home. Thomas rushes out to collect the bag and return it to her, while de Noailles heads for the palace, ready to denounce Evelyn upon her arrival. Thomas collects the bag and sets off to find Evelyn, who pops back into existence as he approaches. She urges the bewildered Leaf not to tell Thomas what he has seen, assuring him that it was not witchcraft, and thanks Thomas for returning her bag and continues onwards to the palace with Leaf. Satisfied, Thomas returns to his home, and informs the shocked Crow that Evelyn was indeed a traitor. They must be alert to the snares that Satan has placed in their path -- but it will be much easier once the queen has fallen...

Queen Mary is not at all as the Doctor expected her to be. He asks Sarah what the people think of her, and she assures him that the average man -- while caring little who is on the throne so long as there is plenty to eat -- understands the Queen's duty to find a husband, honour and obey him. The Doctor admits that he is not wed, but suggests that doctors, like priests, should devote their time to the common good. Sarah seems to be slightly put off by this comment, and reminds him that under Edward, clergymen were permitted to take wives. These laws, however, have been repealed by Mary, and those who wed in good faith now find their marriages made unlawful and their children bastards in the eyes of God. The Doctor would hope that God takes good intentions into account -- he has to. If the Protestants do not repent and hundreds are burnt at the stake, and if Elizabeth then takes the throne, what will history have to say about Mary? If the Doctor had, in his time, caused whole races to die, caused good people to lose their faith and sanity, or had allowed millions to be enslaved because he failed to act... would he still be a good person, if he had acted for the right reasons? Sarah is unsure how to respond, but nevertheless gives her honest answer -- she believes that the Doctor is a good man, and that God would forgive him.

Evelyn is reunited with the Doctor, who insists that given the immense size of the Universe, missing his target by only a few years is insignificant; even if those few years did nearly get Evelyn killed. Sarah takes them in to see Queen Mary and leaves to fetch refreshments, but de Noailles then bursts in with news of a plot against Mary's life; the Doctor has wormed his way into her favour and intends to poison her with the pills brought by Evelyn. Evelyn is forced to turn out her bag and present the aspirin for inspection, and she realizes that Reverend Thomas has betrayed her. The Doctor, however, assures the queen that whereas the aspirin may cause death if taken in large quantities, they are beneficial if taken in small doses. Evelyn takes a pill herself to demonstrate, and although de Noailles insists that it's a trick, he clearly realizes that he's on to a loser. In fact, Mary takes one of the analgesics herself, and finds that her aches and pains have quite vanished. Humiliated and thoroughly discredited, de Noailles storms out in a huff and angrily confronts the Reverend for making him seem a fool. And to make matters worse, although the queen appeared to take no notice, Evelyn mentioned Thomas' name before her. They must act immediately -- and thanks to something that Evelyn told him earlier, Thomas knows exactly what to do...

As Evelyn and Leaf wait outside the palace, the Doctor speaks with Mary, who is feeling better than she has for years. Convinced that the Doctor has been sent to her by God, she decides to reward him by arranging his marriage to her lady-in-waiting, Sarah. The Doctor is taken aback, but can't think of any way out of it, and reluctantly leaves the delighted queen to make the arrangements. But Sarah is not available for some reason, and the queen therefore summons a guard to attend to another matter -- the arrest of the Reverend Thomas whom Evelyn had mentioned. Meanwhile, Thomas meets with a co-conspirator and hands over a potion, warning that only a few drops must be administered -- but guards then arrive to arrest him, and as his co-conspirator flees without being spotted, Thomas rushes to de Noailles for help. But the Bishop's sole aim was to get a ruler on the English throne who would favour France over Spain; he is still a Catholic, and will not risk himself to save the life of a Protestant. Thomas threatens to admit everything, but who would believe that a Catholic bishop and the brother of the French ambassador was plotting with a Protestant to murder the English queen? Thomas flees, knowing that he is a doomed man.

Guards suddenly arrive to arrest the Doctor and his friends for heresy, for the Reverend Thomas Smith has been arrested and has named the Doctor as his co-conspirator in a plot to deny the one true religion. The Doctor cannot honestly claim to have attended Mass in this parish, and he, Evelyn, Leaf and Crow are all taken to the Tower to await execution. Somehow they must find a way to escape and warn the Queen of the danger -- for if she dies in January 1555 instead of November 1558, history will go awry and Evelyn will cease to exist. But how can they possibly escape the Tower of London? Long experience of coming home late at night after student parties has taught Evelyn how to pick locks, but this particular cell is barred from the outside, and the Doctor refuses to lure in the guard and hit him over the head. Their only hope is to work out how Thomas intends to kill the queen; she may not know of their predicament yet, and if they can save her life and convince her that the evidence against them is flimsy at best, perhaps she will pardon them.

Evelyn tries to remember all she can about Thomas, admitting that she never trusted him; he's far too good-looking, blond and blue-eyed and utterly devoted to his cause. The obvious weapon is poison -- Evelyn's painkillers may even have inspired the idea -- but how do they intend to administer it? Mary has tasters to protect her from poisoned food and drink, and even if she were to keep a drink by her bedside table, there is no way to guarantee that a lady-in-waiting would not drink it herself. The only thing that they can count on the queen to do regularly is to attend Mass... and de Noailles will be attending it with her, and will be in just the right position to slip poison into the sacraments. Convinced that this is the means by which the queen will be killed, the Doctor tries to convince his jailer that he has proof of a plot against Mary's life. The jailer ignores him, until Evelyn suddenly collapses, feeling faint. The nexus point is erasing her from history -- or so the Doctor assumes until the jailer enters to see what's going on, and Evelyn orders the Doctor to hit him with a chair. The Doctor reluctantly does so, and he and Evelyn flee for the Thames, hoping to reach the palace before the queen enters Mass.

Sarah Whiteside is waiting for the queen to emerge from Mass when the Doctor and Evelyn arrive, and she stops them from entering; interrupting the holy services would be cause for excommunication. The Doctor realizes that neither de Noailles nor Thomas Smith, both men of God, would poison the holy sacraments... and just as Mary and de Noailles emerge from Mass, the Doctor puts the names together and realizes the truth. He now understands why Sarah felt so strongly about the marriage of the clergy -- under the reign of Edward, Sarah Whiteside married the Reverend Thomas Smith. She is forced to admit that this is true, and that Thomas had given her a potion which he claimed would give the queen dreams that would show her the error of her ways. The infuriated Mary orders that Sarah be taken away to be executed, but the Doctor pleads for mercy; Sarah only acted in the interests of her husband, whom she was bound by law to obey, and would never knowingly have harmed the Queen. Mary is not swayed until the Doctor also reveals that Sarah is with child, and for the sake of her own unborn child, the queen reluctantly agrees to place Sarah under arrest. At the Doctor's request, she sends Sarah to attend Elizabeth, who is also under house arrest. de Noailles is only too happy to arrange the matter for her, but Mary, angrily sends them all from her sight, including the Doctor and Evelyn. As she goes, Sarah tells the Doctor that she will name her son after him.

The Doctor understands Mary's anger and fear; someone very close to her nearly betrayed and killed her, and she will never trust anyone again. Even her husband ignores her, and she is pinning all of her hopes on a baby which she probably knows deep down that she does not have. History appears to have been set on course; John Whiteside-Smith's father will be executed while his mother serves in Elizabeth's household. Evelyn shuts off the Doctor's stabilisation unit -- but she claims to be suffering from a headache, and insists that the Doctor must rescue Leaf and Crow before history is put right. The Doctor knows better, but takes her to the Tower anyway. Leaf and Crow are shocked when the TARDIS materializes in their cell, but the Doctor and Evelyn assure them that they're not devils from Hell nor angels sent from Heaven; they're just here to offer Leaf and Crow -- and Crow's family -- a trip to one of the safe Protestant cities, such as Geneva or Frankfurt. There will be plenty of other exiles to keep them company, and in three years time, Elizabeth will succeed Mary, and they will be able to return home.

Mary has Thomas Smith brought before her, and, terrified, he begs for mercy and promises to do anything she wants if she will pardon him. She orders him to recant his false religion and tell the other Protestants that their way leads only to eternal suffering... but even in the face of death, he will not do this. His way is the true religion, no Protestant is a heretic, and when he dies the Lord will take him to His side. Furious, Mary sends him to be burnt at the stake, and drives the supposedly sympathetic de Noailles from her side as well. There is only one man she trusts to tell her she is doing the right thing. But the Doctor has gone.