The arrival of the TARDIS in Paris, France in 1572 places its occupants, the First Doctor and Steven Taylor, in a dangerous situation. Tensions between Protestants and Catholics are at fever pitch in the city –- with younger hotheads like Gaston, Viscount de Lerans, a Protestant Huguenot nobleman, and Simon Duval, a Catholic, drawn into violent confrontation in a tavern. Despite the danger, the Doctor heads off alone to visit the apothecary Charles Preslin, leaving Steven to drink alone but warning him to keep out of trouble. Moments later, Steven attracts the attention of the landlord of the tavern for not settling his bill, but is helped out financially by Nicholas Muss, a less aggressive Huguenot, who welcomes him to his party of drinkers. Muss explains that the marriage of the Protestant Prince Henri of Navarre, Gaston’s employer, to the Catholic Princess Marguerite de Valois, the sister of the King, is the cause of the heightened tension in Paris. While Steven, Gaston and Nicholas are wandering home, they find a frightened serving girl, Anne Chaplet, who is terrified of being pressed into the service of the Catholic Abbot of Amboise. Anne is also scared because she has heard some guards in the pay of the Cardinal mention how a religious massacre of Huguenots back in her home town of Wassy a decade earlier could now be replicated in Paris. To protect her and her knowledge, Nicholas arranges for Anne to go into the service of his master, Admiral Gaspard de Coligny, the most senior Protestant adviser at the Royal Court. Steven also stays with the Admiral to avoid the curfew in the city, as the Doctor has not returned to the tavern as arranged.
The next day, the Abbot of Amboise has arrived at his Parisian residence. He bears the exact likeness and voice of the Doctor. He is a religious zealot who acts as enforcer to the ever-absent Cardinal of Lorraine. The Abbot is about to journey to Paris to conduct a metaphorical witch-hunt against all heresy, including the apothecaries and the Huguenots. He sends his secretary, Roger Colbert, out to track down the missing Anne Chaplet, convinced she has worked out the threat to the Protestants. Colbert makes for de Coligny’s house and tries to convince Nicholas, Gaston, and Steven that Anne has been over-creative in her interpretation of what she heard. A little later, Steven spies Colbert talking to the Abbot about the situation, and is stunned that the cleric seems to be the Doctor. When Steven and Nicholas track down Preslin’s shop to try and find the Doctor, they discover it has been closed since Preslin was arrested for heresy two years before. This news makes Nicholas suspicious that Steven is a spy in the employee of the Doctor/Abbot.
In the Council of France a power struggle is in place between the impassioned, Catholic Tavannes, Marshal of France, and the more cautious Admiral de Coligny, who is trying to persuade the Court to back the Dutch in their war against Spain. By the end of the Council meeting, de Coligny is confident his advice has been taken.
Steven has now fallen out with and evaded Nicholas Muss, taking his chances in the streets of Paris alone. He heads for the Abbot’s house, believing him to be the Doctor, and hides there while Tavannes, Duval and Colbert meet to discuss their plans. The "Sea Beggar dies tomorrow" assures Tavannes, as an assassin has been engaged to kill him when he departs the Royal Council in the Louvre. The Sea Beggar is a codename for de Coligny, but the conspirators do not reveal this. It is an order direct from Catherine de' Medici, the Queen Mother, and the real power in France as her son, the weak King Charles IX of France, is much in awe of her power and authority. With night falling again, Steven heads out again and finds Anne following him. She has been dismissed from service for protesting Steven’s innocence in the Catholic plot. They hide the night at Preslin’s empty shop then determine to try and find the identity of the Sea Beggar. As they start their search they agree that if they become separated they will return to Preslin's shop.
When the early Council resumes at the Louvre the next morning, Tavannes and de Coligny are still locked in conflict, and the King now seems less tempted by de Coligny’s arguments for entering a war. They also argue about domestic matters, with de Coligny urging more action to protect the Huguenots. In doing so he insults the Queen Mother, who leaves the Council Chamber in a fury. The Council is then dissolved for two days until St Bartholomew’s Day.
Steven and Anne call upon the Abbot, where he learns both that the Doctor is not the Abbot and the identity of the Sea Beggar. The pair flee before Anne can be confined, alerting the Abbot, Tavannes and Colbert of their danger since they evidently know too much. Steven and Anne make contact with Nicholas Muss and warn him the assassination of his master is about to take place. Nicholas bolts off and witnesses the assassination attempt, but fortunately de Coligny is merely wounded.
Tavannes believes the bungled assassination is the fault of the Abbot, who has become a liability, and the cleric is placed under arrest, suspected of being an impostor. At the Court, the King is also enraged by news of the assassination attempt – and vows the culprit will be caught. In response he calls a meeting of the Council and urges Tavannes to take measures to control the lawlessness on the streets, warning him that if anything further happens to the Admiral then he will be held responsible. The King also turns against the Queen Mother, believing her to be bloodied by the assassination attempt, and threatens her with a convent unless she desists in the political machinations. She responds by warning him that his own throne is not safe now that the Protestant Prince Henri is in line for the throne, sowing seeds of doubt in his mind.
De Coligny has meanwhile been moved to his house, and a surgeon called, and as Steven and Nicholas tend to him they too receive some shocking news: it seems the Abbot of Amboise has died! Steven is distraught, still partly convinced that the Doctor has adopted the Abbot’s guise, heads to the Abbot’s lodgings and sees the dead body there. It seems the Abbot has been assassinated too, inflaming the Catholic mob outside the house, which does not disappoint the real culprits, Colbert and Tavannes.
On the following day, Steven heads back to Preslin’s shop in a low mood and is reunited with Anne. A little later he is shocked when the Doctor himself arrives, brooking no criticism of his absence, and is very insistent that he and Steven must depart the city as soon as possible. Anne is sent to her aunt’s house, with a warning from the Doctor that she must stay behind doors for the next day. She heads off in fear and tears, while Steven and the Doctor head across the city.
The Queen Mother has now persuaded the King that the Huguenots are a threat to his reign, and has signed an edict authorising a Huguenot massacre over the next twenty-four hours. She also insists that that the massacre is not confined to a list drawn up by Tavannes, containing supposed enemies of the state, but rather is aimed at all Protestants within the city walls – bar Prince Henri himself, despite his supposed pretensions to the throne. The King also commands the gates to the city be locked. Simon Duval and Colbert greet the coming massacre with more glee and bloodlust than that displayed by Tavannes, who fears the Queen Mother has gone too far.
The Doctor and Steven make it to the TARDIS just as the curfew is falling and depart as the massacre begins. Steven is in a foul mood, worried for Anne and his friends, and angry that the Doctor made him leave. The Doctor insists that history could not be changed: ten thousand Huguenots will die in Paris alone during the massacre, which will last for several weeks. De Coligny and Nicholas Muss will be amongst the dead, and possibly Anne too. Steven cannot accept that the Doctor had to leave Anne behind, and is so disgusted with his colleague that he determines to leave his company. When the TARDIS lands Steven offers a terse goodbye and ventures out into a woodland area. The Doctor is left totally alone for the first time, and reflects on the other companions that have travelled with him and then left him. Going home is not an option either...
The TARDIS has arrived in 1966 and a young girl enters the vehicle thinking it to be a Police Box on Wimbledon Common. A small child has been hurt in a road accident and she wishes to make a call. Steven arrives back too, saying that policemen are approaching, and his heart softens when the young woman introduces herself as Dorothea or Dodo Chaplet. It looks like Anne could have survived the massacre after all.
The Doctor, hearing Steven's warning of the approaching policemen, hurriedly teleports the TARDIS away, not noticing until after it has left 1966 that Dodo is still aboard. Steven informs her that there's no way back, and "we could land anywhere," but Dodo seems either unworried or simply doesn't believe him. She says she is an orphan who lives with her great aunt (also reminiscent of Anne), and thus has few ties, as the TARDIS continues to hum, hurtling them toward the next great adventure.