November, 1604. King James I arrives in London for the opening of Parliament, but much to Sir Robert Cecil's frustration, rather than prepare his speech for the opening, James spends his time carousing with his latest favourite, a sallow young man named Robert Hay. Cecil is convinced that the Catholics are plotting to overthrow the Protestant James, and since the King will not listen to him, Cecil has laid secret plans with a mysterious hooded figure known only as the Spaniard...

The TARDIS also arrives in London, and Ian and Barbara ask the Doctor's permission to visit the Globe Theatre. The Doctor, dismissing their request as nothing more than tourism, allows them to go their own way, while he and Vicki set off for Whitehall Palace to observe the translation of the King James Bible. At the Doctor's suggestion, Vicki disguises herself as a boy to avoid unwanted attention. Claiming to be holy pilgrims, they bluff their way past the guards and into the company of the elderly translators Haldann and Otley, who are spending more time arguing with each other than concentrating upon their work. Cecil is suspicions when the new arrivals claim to have lost their papers in a struggle with ruffians on the road, and invites them to attend a dinner with the King. They do so, and Vicki inadvertently attracts the attention of King James, who is delighted by young "Victor"'s robust and youthful appearance. He is already beginning to lose interest in young Hay. Cecil once again demands that the King address the Catholic problem in his speech to Parliament -- and Vicki notes with suspicion the Doctor's close observance of their argument.

Prevented from reaching the Globe by crowds watching a bear-baiting, Ian and Barbara shelter in a tavern along with cobblers Firking and Hodge and a mysterious hooded figure. As they discuss the Doctor's odd behaviour back at the Ship, the hooded figure leaves, apparently dropping a note on his way out. Ian and Barbara read the note but are unable to make sense of it; it appears to be a random collection of words in French, Italian and German. The tavern's serving wench, Sybil, then arrives, followed by two Catholics who appear to be waiting for someone. The man named Rob seems to see enemies in every corner, and when Firking and Hodge bait them a fight breaks out. Ian and Barbara attempt to get out of the tavern, but Rob takes Barbara hostage in order to escape, hitting her on the back of the head when she struggles. Ian loses them in the streets outside, and the abashed Firking and Hodge offer their assistance should he need it. The concussed Barbara, meanwhile, apologises to the strangers for reading their note, and despite his level-headed companion's urging, Rob Catesby decides to question her back at their lodgings to find out how much she knows. When Barbara hears Catesby refer to his companion as Johnson, she realizes that the level-headed Johnson is in fact Guy Fawkes.

Cecil soon guesses the "Victor" is really a girl, and when he meets with the Spaniard that night, the Spaniard reports that his note to Catesby was intercepted by a young couple who spoke of a doctor and of travelling by ship. Cecil concludes that the Doctor and his ward are spies from Holland, and the Spaniard decides to kill them both. He manages to enter the palace undetected, but the Doctor fights him off with Vicki's help and in the process notes a strange rectangular symbol on the assassin's knife. Cecil, meanwhile, informs the King that the Doctor and "Victor" has left, and the King is so despondent at his loss that he drives Cecil out, refusing to discuss the speech with him. When the Doctor and Vicki find Hay comforting James the next day, James is delighted to see them, and concludes that Cecil must have been mistaken, leading the Doctor to deduce that Cecil dispatched the assassin. At James' request, Vicki is taken to be fitted with suitable apparel for a courtier, and her plastic sandal, while causing some bemusement, is nevertheless sent to the nearest shoemakers' to be copied. The Chamberlain frets over these constant delays to his preparations for the opening of Parliament on November 5, and Vicki, recognizing the date, finally realizes why the Doctor has really brought her here.

Barbara recovers to find Fawkes tending to her. Despite his reluctance to kill an innocent woman he must know how she knew his real name, and, realizing she has no choice, she tells him that she's a traveller in time. She tells Fawkes all she knows about the Gunpowder Plot in order to prove her story, but then the eavesdropping Catesby bursts in, accuses her of witchcraft and attempts to kill her. Fawkes knocks him out and takes Barbara to safety in a nearby inn, where she sleeps off the rest of her concussion; despite the care he has shown her, however, she knows she cannot risk changing history by warning him of the horrible death fate has in store for him. When Catesby awakens, he is suffering from concussion himself and goes nearly mad with paranoia, convinced that Fawkes has betrayed him. Ian, meanwhile, goes to Firking and Hodge for help, sees Vicki's plastic sandal being brought in, and thus learns that the Doctor and Vicki must be at the palace. Sybil, the maid from the tavern, arrives to inform Ian that she's learned that Barbara was kidnapped by Robert Catesby; Ian, recognizing the name, sets off for the cellars of Parliament to find him. Firking and Hodge, assuming that Ian must be on a secret mission for the King, follow him, hoping to come into some reward for assisting him.

Cecil is shocked to see the Doctor still attending Haldann and Otley, and when the Doctor drops deliberate hints about a plot brewing, Cecil's furious reaction confirms the Doctor's suspicion; Cecil himself has set the Gunpowder Plot in motion, in order to expose it and provide an excuse for punitive measures against the Catholics. Vicki then confronts the Doctor, having realized that he's really come to investigate the Plot, and convinced that he only asked her to accompany him because she's too trusting to ask questions. She steals the TARDIS key from him and sets off to return to the ship, but is confronted on the way out by Hay, who seems murderously jealous that she has replaced him as the King's new favourite. She manages to get away from him, but eventually realizes that she will be stopped by the guards before she can get out of the palace grounds. Dejected, she is about to return to the Doctor when she catches a glimpse of the hooded assassin who attacked them earlier. She follows the Spaniard to a tree in the grounds, which turns out to be a false entrance to a network of underground tunnels and the Spaniard's secret underground base. There, she is captured by the Spaniard, who turns out to be Hay in disguise. He drugs Vicki and questions her, and under his influence, she reveals that the Doctor travels through time and space.

Cecil alerts the Chamberlain to the fact that prominent Catholic Sir Thomas Percy has rented rooms directly beneath Parliament itself, and the Chamberlain, already run off his feet, agrees to investigate it mainly to stop Cecil from bothering him. The Doctor then confronts Cecil, revealing that he's already guessed most of his plan -- including certain details which seem to have escaped Cecil's attention. Cecil may believe that his ally the Spaniard is assisting him for the money, but it's only thanks to Cecil's surreptitious assistance that Catesby's plan has progressed as far as it has. What if the Spaniard in fact intends to prevent Cecil from delivering his warning in time? Cecil, realizing that the Doctor has an excellent point, leads him to his meeting place with the Spaniard, where they discover the tree and enter the tunnel systems. Hay, however, is waiting for them with two eunuchs and the hypnotised Vicki; he reveals himself to be a master of a grand order of mystic sorcerers, and Vicki's tales of space-time travel have convinced him that the Doctor is a Grand Behemoth of his own order. The Doctor plays along in order to learn more, and finds that Hay has manipulated both sides of the Gunpowder Plot in order to ensure its success; the destruction of Parliament will lead to anarchy and chaos, and the Brotherhood will rise to power amongst the ashes.

Ian manages to locate the cellars where the gunpowder is being stored, just as the delirious Catesby accuses Fawkes of treachery and stabs him through the heart, killing him. Before Ian can do anything about it, he is captured by the other conspirators, including Thomas Percy. The Chamberlain arrives to investigate Cecil's accusations, but as he's already flustered and doesn't want to cause trouble, Percy is easily able to convince him that there's nothing to worry about. As the reassured Chamberlain goes on his way, Percy, believing that Ian is a spy for Cecil, ties him up in the cellar with the gunpowder, to die when the barrels explode. Firking and Hodge, realizing that Ian is in danger, set off to collect weapons and rescue him.

The Doctor convinces Hay to let Cecil live as a scapegoat, and to find Ian and Barbara and bring them to the tunnels. Hay has been observing Ian and Barbara in disguise to determine what part they played in the Plot, but now concludes that the grand masters of his order were testing him. The Doctor and Vicki return to the palace, where they try to work out a plan to stop Hay and rescue Cecil without besmirching Cecil's name; since Cecil is primarily responsible for putting King James on the throne, any hint of scandal could topple the monarchy. King James then contacts the Doctor, claiming that a devilish, humming wooden box has been brought before the Lord Mayor of London; it was found apparently abandoned and was taken to be chopped up for firewood, but no axe can damage it, and it is believed to be possessed. The King orders the Doctor to perform an exorcism, and the Doctor, only too delighted to do so, sends Vicki to return to the tunnels and wait for Ian and Barbara while he prepares himself.

Barbara, hearing rumours of the mysterious box, arrives at the Guildhall where the TARDIS is being held; there, she meets Sybil, who leads her into the secret tunnels which she claims she uses as a short-cut to work. Once there they find Vicki, who explains to Barbara how the Doctor is tricking Hay -- and realizes too late that "Sybil" is Hay in yet another disguise. She and Barbara overpower the furious Hay, but while Vicki bluffs Hay's eunuchs into releasing Cecil, Hay recovers and flees. Vicki and Barbara return to the palace, where the Doctor takes them to the Guildhall for the exorcism, trying to stretch matters out until Cecil arrives with news of the plot. Meanwhile, Firking and Hodge arrive at the cellars to rescue Ian, and when the recovering Hay stumbles in, determined to light the powder and destroy Parliament as planned, they are able to overpower him. Cecil arrives and arrests Hay, intending to charge him under the name of Guy Fawkes and torture a confession out of him; King James, who has already lost interest in Hay, will never know the truth. Ian takes news of the plot to King James at the Guildhall, and in the confusion which follows, he and his companions enter the TARDIS and depart.