France, 1242 AD. Papal contender Chretien d’Alsace is killed by mercenaries hired from Louis de Citeaux by Francisco Guzman, d’Alsace’s rival for the Papacy. Three of the mercenaries encounter and attack Guy de Carnac, a former Knight Templar on his way to Béziers to take the coin of Phillipe de Montfort. Guy kills two of them and leaves the third for dead, and continues on to Béziers, where de Montfort is serving de Citeaux until he can reclaim the ancestral lands his brother gave in fealty to the King. Guy takes Phillipe’s coin, but is horrified when he sees Guzman preparing to burn down a church in which heretics have claimed sanctuary, even though fellow Christians are trapped inside with them. The man he left for dead then recognises him and informs Guzman, and Guy is forced to fight his way out of Béziers. Guzman and de Citeaux order Phillipe to ensure that Guy doesn’t live to reveal what he has seen, and Phillipe, humiliated by Guy’s betrayal, vows revenge. Outside the city, Guy spends the night with refugees who hope to shelter from the religious war in the Roc of the Cathares. In exchange for shelter, he offers to protect them during their flight; there are three Knights Templar in the vicinity, but they will provide no help, as they claim that they are simply neutral observers. In fact, they are secretly intercepting messages from Louis’ spy within the Roc, and editing them to serve their own agenda.

Shortly after leaving Gadrell Major, the TARDIS falls into the gravity well of a black star, and the Doctor and Benny abandon ship in the Jade Pagoda while the TARDIS passes through its temporal distortion field. They arrive at a village where Catholic soldiers are about to burn a heretic at the stake, and Benny insists that they rescue him before realising that they too are surrounded. The Doctor, quicker on the uptake, accuses her of heresy and “accidentally” gets in the soldiers’ way as she flees. He upbraids the soldiers for their carelessness, claiming to be an important emissary from the Scottish court, but this backfires when the sergeant, eager to make amends, offers to escort him to Béziers. There, the Doctor bluffs his way into the company of Guzman and de Citeaux, who are torturing a captured Cathare to learn the location of the Roc’s secret entrance. Certain that Benny will find sanctuary in the Roc, the Doctor knocks the prisoner unconscious, making it appear that he has died under torture. The Cathare’s body is left unattended, and when he wakes, he escapes -- with a tracker attached to him, so the Doctor can follow him and locate Benny.

Benny meets Guy when she joins the refugees heading for the Roc. At first, she finds him to be moody and uncommunicative, but when the refugees are attacked by bandits, Guy and Benny both help to fight them off and are impressed by the other’s fighting skills. The refugees are guided to the Roc’s secret entrance by conscripted Catholic soldiers, locals with more loyalty to their families than their faith, but once inside they learn that the Roc is already dangerously overcrowded due to Parfait Girard’s refusal to turn away anyone who needs assistance. The situation has become untenable, and Girard has had no choice but to negotiate a surrender; the Cathares will soon make their peace with Amor and open the doors to the besieging Catholic army. Nevertheless, they still require a strong defense until that time, and Girard, noting Guy’s aptitude with weapons and discipline, asks him to train the defenders until the time comes for them to surrender. Guy accepts this task, while Benny assists Parfaits Jeanne and Giselle in the Roc’s hospital.

The Doctor accompanies de Citeaux and Guzman to the Roc to witness the last days of the siege, while surreptitiously using his tracer to follow the escaped prisoner’s path. Phillipe catches the Doctor near the river, apparently trying to locate the Cathare’s trail, and reveals that he knows the Doctor helped the prisoner to escape; however, he agrees to remain silent in exchange for the Doctor’s help. If Phillipe can prove that de Citeaux allowed a heretic to escape from under his very nose, he will be disgraced and Phillipe can claim the Holy See’s support for himself. With their backing, he will reclaim his ancestral lands and set up an independent principality beside France, with himself as ruler. The Doctor realises that if Phillipe succeeds, history will be changed, and the Doctor will be responsible.

The prisoner reaches the Roc, but dies of his wounds after telling Benny that the Doctor helped him. Benny decides to rescue the Doctor, and enlists Guy’s help, as he’s the only person in the Roc she feels comfortable talking to. Internal strife has developed within the Roc in these last days; Parfait Jeanne, who has personal duties above and beyond those of her faith, has seen how the wounded in the hospital struggle to cling to life, and does not agree that they should be allowed to pass on peacefully into the next life. The young apothecary, Robert, seems to regard Guy as a hero, but the Castellan isn’t pleased that the defense of the Roc has been left in the hands of a mercenary. Benny witnesses a sacred ceremony involving a skull which the Cathares believe represents the inevitable future of all matter; they are unaware that, in fact, one of their most sacred relics is a fake which de Citeaux intends to expose after the fall of the Roc in order to shatter their faith.

Benny, Guy and their friends “rescue” the Doctor, much to his despair, as he still hasn’t figured out a way to stop Phillipe without killing him. Nevertheless, he flees with the others, leaving Guzman and de Citeaux under the impression that he’s been kidnapped by the heretics. Back in the Roc, Benny, thankful for Guy’s help and growing to trust him, tells him about her mother’s death in wartime, but as they talk they hear Girard screaming, and find that he has apparently stabbed himself to death in a room barred from the inside. The Doctor, however, wonders why a man committing suicide would scream, and when he examines the fingerprints on the blade he finds that someone other than Girard handled it. They decide to question the Castellan, who was seen arguing with Girard over Guy’s position of authority; even if he isn’t guilty, he may know if there are any secret passages in the Roc which the killer could have used to escape without being spotted. The Castellan, however, has seen someone throwing a message over the parapets of the Roc, and has gone to warn Parfait Jeanne that there is a spy in their midst. By the time Benny and the Doctor find the Castellan, he too has been struck over the head and then hanged.

Since the Cathares have run out of supplies, it seems that they will be forced to send the refugees out of the Roc without provisions. Benny and Guy offer to lead a raiding party to a nearby aubaine storage house, where they find that the elderly reeve has died of the cold. They are thus able to loot it, but run out of time to return to the Roc and must spend the night there. As Benny stands watch, she sees Guy waking from a nightmare, and he explains that he used to be a Templar until his sister was raped by another knight and took her own life. He deserted his post to hunt down his enemy, only to find that he had been killed while fighting a band of Saracens; thus, Guy’s enemy died honourably, while Guy was expelled from the order of the Templars in disgrace. The next day, some of Guy’s friends leave the Roc to search for the missing Guy and Benny, but run into Phillipe de Montfort and his soldiers, who are trying to find out why the Doctor was so interested in the river earlier. Guy and Benny stumble across the battle on their way back, and in the course of the fighting, Guy kills Phillipe.

The Doctor works out how Girard’s door was barred from the inside by the killer; a poker was used to balance the desk against the bar, and when the door was released from the outside, the falling poker knocked the bar back into place as the desk fell backwards. Having solved this, the Doctor studies the Castellan’s notes and finds that he had been studying the walls of the Roc for weak points -- but had suddenly stopped upon reaching the apothecary’s garden. The Doctor’s suspicions are confirmed when he examines the garden for himself. When Guy and Benny arrive the Doctor leads them to the library to search for the Cathares’ mysterious relic, certain that it is the key to the murders. They find a skull which the Cathares believe to be the skull of Jesus Christ himself, proof that the resurrection was a myth and that all matter is dust. The Doctor then reveals that the apothecary Robert is Louis de Citeaux’s spy, as the Castellan had realised when he noticed that the garden was not planted with proper apothecary’s herbs.

Guy kills Robert as he tries to escape, but Parfait Jeanne then shoots Guy in the shoulder with an arrow, revealing herself to be the murderer. Before she became a Parfait she had given birth to two sons, but she never revealed their existence to Girard for fear he would expel her from the Order. Her sons’ farm has been looted, leaving them as serfs with no master, and as she knows the Roc is doomed to fall anyway she intends to sell the relic for money with which to buy her sons’ freedom. She killed Girard when he refused to tell her the location of the relic, and killed the Castellan in panic when he came to her after spotting Robert and told her, erroneously, that he knew who the killer was. Benny distracts and overpowers Jeanne, who is arrested and locked up in the Roc’s cellars; there, Benny avenges Guy’s injury by telling Jeanne exactly what the next few centuries hold in store -- death, persecution and religious warfare, and the end of the Cathares. Meanwhile, a monitor which the Doctor has been carrying alerts him to the return of the TARDIS; it is now safe for him and Benny to leave.

Robert’s last message reveals to Guzman that the Doctor has been helping the heretics. Guzman blames Louis for the humiliation, but, knowing that Louis can still expose him for d’Alsace’s murder if he acts openly, arranges for Louis to be shot with an arrow taken from a dead heretic. Meanwhile, in the Roc, Parfait Hugues asks the Doctor to help him take the relic to safety, and the Doctor and Benny agree to escort him to the village where the TARDIS is now waiting for them. As the refugees evacuate, Guy, knowing that Benny will only be hurt if he remains with her, decides to shadow her until he’s sure she’s safe, and then slip away without saying goodbye. As soon as the refugees have gone, Parfait Giselle opens the doors to the Catholic forces. Guzman, infuriated to learn that both Guy and the fake skull have slipped out of his hands, orders that the Roc be burnt with the heretics still inside. He is unaware that the Templars plan to expose him for the murders of both d’Alsace and de Citeaux; they have their own candidate in mind for the Papacy, and they had been editing Robert’s messages to ensure that the siege continued until their rivals eliminated each other.

The Templars meet Hugues at the village, and take the skull for safekeeping. But they have been followed by de Citeaux’s soldiers, who kill Hugues and pursue the Doctor and Benny while the Templars escape. Guy arrives just in time to save the Doctor and Benny, but as Benny asks him to come to safety with them, another group of soldiers enters the village. Guy sends the Doctor and Benny on ahead and sets the bridge on fire, trapping himself and the enemy soldiers in the burning village while Benny escapes. The Doctor drags the protesting Benny into the TARDIS and takes it a few minutes forward in time, to find that the fire has burned itself out and left the village full of smouldering corpses. Benny, realising too late that she had fallen in love with Guy, knows that there’s no way he could have survived, but doesn’t want to confirm it by looking for the body. The Doctor sadly takes her away.