It is December of 1648, and Colonel Thomas Pride and Lord Grey of Groby are turning away duly elected officials from the House of Commons, allowing past only those who will vote to ensure King Charles faces trial for treason. It seems that history will soon record an act of regicide. Meanwhile, William Kemp, the owner of a local inn named the World Turn'd Upside Down, lets out his upper room to a group of strangers, and his daughter Frances comes to believe that something treasonous is afoot. She is in love with Roundhead captain Thomas Culpeper, but is unwilling to tell her father, who has become sullen and bitter ever since his son Arthur was killed while fighting for the Cavaliers on Marston Moor.

The TARDIS materializes nearby, and the Doctor fetches a children's history book from the TARDIS to ensure that he and his companions are up to speed on the period. Realizing that Ben and Polly have been teasing Jamie about his lack of knowledge, he sends them off to explore while he and Jamie set off on their own. While making for the Christmas festival on the frozen Thames, the Doctor and Jamie make a new friend when they save a saltpetre man named Nathaniel Scrope from a beating by group of bullies who overheard him making disparaging remarks about the King. The Doctor and Jamie enjoy themselves at the festivities, but on their way back to the TARDIS they are confronted by a suspicious watchman who accuses Jamie of being a deserter. Threatened with torture, the Doctor and Jamie claim to be seers with the power to look into the future. They are thus taken to Oliver Cromwell, who is fascinated by the mystical and asks them to tell him what the future holds. Sir John Thurloe decides to keep them under observation until he can determine what their true agenda is. In the confusion, the Doctor realizes that somewhere along the line he's lost his copy of the history book; if it falls into the wrong hands, somebody could use its information to change the future...

Ben and Polly stop in at the World Turn'd Upside Down, where Ben foolishly suggests out loud that perhaps he and Polly are in time to see King Charles get beheaded. As they leave the pub they are set upon, and Ben is knocked out while Polly is dragged upstairs to explain herself to the conspirators. She manages to convince them that her friend was just talking idly, and they agree to let her go, but young Christopher Whyte decides to follow her to find out what she knows. Ben awakens to find that while unconscious he has been press-ganged aboard the Teazer, a ship heading for Amsterdam under the Dutch Captain Stanislaus. Isaac Ashdown, the man who brought Ben on board, seems friendly enough, and warns Ben not to pay close attention to Stanislaus' business or to his mysterious passenger, Richard Godley.

Polly, unable to find her friends anywhere, returns to the inn, where she meets Frances. Frances offers to leave a note for Thomas asking him to help look for Polly's friends, but Whyte finds the note and learns of Frances' connection to the Roundheads. Kemp brings her before the conspirators, and their leader, Sir John Copper, orders her to question Culpeper about Oliver Cromwell's movements and his plans for the King. Broken-hearted, she has no choice but to obey. Whyte, meanwhile, contacts Polly and claims that her friends are being held in Hurst Castle, where the King is also being held prisoner; if she helps to break him free, they will reunite her with her friends. Polly reluctantly agrees to help, and is thus substituted for a serving girl and smuggled into the castle. As the conspirators expected, the King's guards are tasting his food before it is taken in to him, and Polly is thus able to drug them. Whyte and Copper enter to lead the King to safety -- but Copper then tries to kill Polly to ensure she can't identify them. Whyte intervenes, but Polly is knocked out, and Whyte has no choice but to leave her behind for the soldiers to find.

The Teazer arrives in Amsterdam, and while in the city on shore leave Ben meets Captain Sally Winter, a pox-scarred woman with a deep grudge against Stanislaus. When she learns that Ben has been forced to work for Stanislaus against his will, she offers to take him back to London on her own ship, the Demeter. Before leaving, however, they decide to investigate Stanislaus' business in Amsterdam; Winter has been studying Stanislaus' movements, and has learned that he has recently been making mysterious journeys to France which she wants explained. They learn only that Stanislaus and Godley are in Amsterdam to collect a "package", but are unable to learn what it is. When they break onto the Teazer, hoping to learn more, Ashdown catches them, but he lets them go, feeling responsible for Ben and having no love for Stanislaus himself. Winter takes Ben back to the Demeter and sets sail, but the Teazer soon appears in hot pursuit; Stanislaus, realizing that his ship was broken into, has tortured the intruders' identity out of Ashdown and now intends to exact revenge.

The Doctor and Jamie see Scropt passing by their apartments and ask him to look around for Ben and Polly. Thurloe then questions them, and, deciding that they mean Cromwell no harm, orders them to ensure Cromwell does not try to rule the country by himself. Some of Cromwell's followers, including Thomas Culpeper, feel that a figurehead is needed for the council of state which is intended to replace the King; Thurloe, however, feels that the monarchy has destroyed itself and should not be replaced with another. He also fears that if Cromwell follows Culpeper's advice, the public will come to believe that he engineered the Civil War in order to seize the crown for himself, in which case the republic Thurloe envisions will never come to be.

Richard Cromwell, Oliver's ineffective son, confronts the Doctor, demanding an explanation; he's found the lost history book and has learned that he is destined to die a failure. Before the Doctor can think of a reasonable explanation he and Jamie are summoned before Oliver, but as Jamie starts to make vague predictions, the King's escape is discovered and Polly is brought before Cromwell to explain herself. She recognizes the Doctor and calls him by name, and the furious Oliver, concluding the Doctor and Jamie were sent to distract him, has them all sent to the Tower. Richard attempts to show him the book, but Oliver will no longer listen to anyone claiming to know the future and drives him from his sight. The Doctor, upon hearing Polly's story, realizes that their intervention may have diverted history onto the wrong course...

The crew of the Teazer boards the Demeter, and while the two crews are fighting, Ben and Winter board the Teazer to take the fight to Stanislaus. They find Stanislaus, Godley, and a third man named van Leeuwenhoek in the captain's cabin, and realize that van Leeuwenhoek himself is the "package". Winter leaves a bomb in the cabin and retreats back to the Demeter, where her crew have repelled the intruders. They leave the Teazer to its fate, but it survives the explosion and Stanislaus sets off in hot pursuit. He pursues the Demeter into the marshes just outside London, where Winter's ship runs aground. Winter, admitting to Ben that she and Stanislaus were lovers until he infected her with the pox, tells him to flee and find his friends while she fights off Stanislaus. She soon gets the upper hand, but Godley, who has no interest in the vendetta, shoots her dead before she can kill Stanislaus.

The King is hiding in a warehouse in London, but despite Copper's urging he refuses to leave the city, informing Copper that before his rescue he had already set plans in motion to assassinate Cromwell. He orders Copper to meet a ship which is now entering the harbour, and Copper in turn orders Frances Kemp to find out about Cromwell's plans for the next few days. She reluctantly elicits the information from Culpeper, but when she takes her information to Copper he assaults her, telling her father she's a whore who would sleep with anyone. Kemp, finally realizing the error of his ways, kicks Copper out of his home and tells him never to return.

Thurloe offers to spare the Doctor and his friends if they tell him all they know about the King's plan to escape, and while telling his story the Doctor mentions having saved Scrope -- who turns out to be an undercover agent, and one of Thurloe's best men. Meanwhile, Scrope rescues Ben from the marshes, and they watch the Teazer dock -- and when "Richard Godley" disembarks, Scrope recognizes him as the King's nephew, Prince Rupert. Unable to follow the conspirators through London, Scrope takes his report to Thurloe. Rupert and his allies, meanwhile, are reunited with the King, and inform him that all has been prepared -- and Whyte learns, to his horror, that the King has assembled an army of Polish mercenaries to retake the throne for him after Cromwell is assassinated.

Ben is reunited with his friends, and Thurloe agrees to let Polly and the Doctor accompany Scrope to the World Turn'd Upside Down to try to find any trace of the conspirators. There, they meet Whyte, who is trying to drink away his horror at the thought of England being overrun by foreign Catholic mercenaries. Although unwilling to betray his King, he does inform them that Cromwell is to be assassinated while addressing the Rump Parliament. He gives Polly a memento to remember him by, but the Doctor tells her that to restore history to the correct path she must follow Whyte and find out where the King is being held. The shattered Richard Cromwell, unable to convince his father to listen to him, returns the Doctor's book to him, and the Doctor hypnotises him to forget what he has read.

The Doctor, Ben and Jamie attend the session of the Rump Parliament where the King's trial is to be voted through, and catch Gustavus van Leeuwenhoek -- brother of the famous Anton -- as he attempts to shoot Cromwell with a dart contaminated with his brother's samples of plague bacilli. The Doctor and Ben overpower him, saving Cromwell's life. Ben accompanies Thurloe when the Roundheads raid the warehouse where the King is hiding, arresting him and his fellow conspirators. Stanislaus tries to flee, but Ben pursues him across the roofs of London until Stanislaus slips and falls to his death. Ben, Polly, Jamie and the Doctor then return to the TARDIS and depart, and the startled Cromwell and Thurloe decide to erase all mention of their visit and the King's near-escape from history. Thurloe arranges to have Culpeper executed for betraying Cromwell to the conspirators through Frances. The King is executed as history dictated -- leaving the way clear for Cromwell to assume leadership of the country.