It is 1792, and the ideals of The French Revolution are beginning to curdle into the Reign of Terror. Hundreds of aristocrats and their supporters are being tried, condemned and sentenced to a bloody fate at the blade of Madame la Guillotine to the bloodthirsty delight of the revolutionary masses. But recently, a league of English noblemen has enacted a series of daring rescues of condemned men, women and children, smuggling them to escape and freedom in England. In particular, the people of both England and France have been transfixed over the identity of the mysterious leader of the league, a brave and daring Master of Disguise who personally rescues the innocent under the noses of the revolutionary guards, and sends taunting notes to the Revolutionary Council. He is known only by the humble wayside flower he has taken as a pseudonym — the Scarlet Pimpernel.
After one such daring rescue, the Countess de Tourney and her two children arrive at an inn near Dover with Sir Andrew Ffoukes and Lord Tony Hastings, two members of the league. But their relief over their safe arrival is soured by the arrival of Lady Marguerite Blakeney, a former actress of the French stage considered to be the cleverest and most fashionable woman in England, and her husband Sir Percy. A rumour has arisen that Lady Blakeney, a sympathiser towards French republicanism, spitefully condemned the Marquis de St. Cyr and his family to death by denouncing them for treason before the Revolutionary Committee. As such, the Countess insults Lady Blakeney and refuses to allow her daughter, an old school friend, to associate with her. After the insult, the Countess's son approaches Sir Percy and offers to allow him to resolve the insult with honour via a duel, but the foppish, imbecilic Sir Percy refuses him, earning his wife's withering contempt.
Marguerite is in Dover to bid farewell to her brother Armand St. Just, a French diplomat and moderate republican. When she does, Marguerite confesses that although she did denounce the St. Cyrs, she did so under false assurances regarding their fate and was utterly horrified when they were executed; she merely wanted to right a wrong the Marquis did them when he had Armand, her only family, viciously beaten for expressing romantic intentions towards the Marquis's daughter. However, her husband learned of the rumour on their wedding night and demanded an explanation. Her feelings hurt and her pride stung by what she saw as her husband's suspicion, Marguerite stubbornly refused to elaborate, and the two have been estranged ever since. Marguerite is convinced that Percy showed a different, more caring and intelligent side to him during their courtship, but since then has treated her with coldness and has acted the dandy interested only in clothes and parties.
After bidding farewell to Armand, Marguerite is surprised to encounter M. Paul Cheuvalin, an old friend from her actress days who has risen in the Revolutionary Committee to become a prominent diplomat and ambassador to England. Cheuvalin is also a spy, however, and is in England to determine the identity of the Scarlet Pimpernel so that he can be captured, tried and executed. He tries to recruit Marguerite's services, convinced that her high-class connections will enable her to investigate the circles he believes the Pimpernel to move in without suspicion. But Marguerite, despite her republican sympathies, is disillusioned by the Revolutionary Committee's brutality and has a romantic, idealistic regard for the Pimpernel, and so refuses him.
Later that night, however, Cheuvalin and his men attack and subdue Sir Anthony and Lord Tony, discovering plans for the rescue of the Count de Tournay — along with evidence implying that Armand St. Just is one of the Scarlet Pimpernel's operatives. Cheuvalin subsequently approaches Marguerite at the opera and forces her to make a Sadistic Choice — either she helps him discover the identity of the Pimpernel, or he passes on the incriminating evidence that will send her brother to the guillotine. Feeling unable to turn to her husband, Marguerite is forced to go along with Cheuvalin's schemes. She subsequently discovers evidence that the Pimpernel will be in attendance at a ball held later that evening by Lord Grenville, the British foreign secretary, and that he will be in a particular supper room at precisely 1am. When Cheuvalin goes to the room, however, he finds only Sir Percy, asleep on a sofa in the corner, leaving Marguerite terrified over the fate of her brother.
Her nerves frayed by her stressful experiences, when she and Sir Percy return home Marguerite confronts Percy over the tension that has arisen between them. She admits the truth behind the rumour of her dealings with the St. Cyrs, and admits that she still cares for her husband and wants to heal the rift between them. Although his attitude remains as cold and distant as before, when she admits that Armand's life is in peril Percy gives her his word that he will do everything in his power to save him. Marguerite comforted by his assurances, but is startled when he suddenly announces that he must leave for the north within the hour. She is further confused when his servants reveal that Percy has in fact boarded his private yacht, apparently sailing to France. After he has gone, Marguerite sneaks into his private study to investigate why, only to discover a ring bearing the symbol of the Scarlet Pimpernel. Putting the evidence she has found and the realisations about her husband she has recently had together, Marguerite is horrified to realise that her husband, who she had previously dismissed as an empty-headed fop, is in fact the Scarlet Pimpernel — and she has enabled Cheuvalin to learn this as well.
Determined to atone for her unwitting betrayal by either rescuing or dying alongside him, Marguerite enlists the help of Sir Andrew to reach France before Cheuvalin. Both parties are waylaid in Dover by a sudden storm, enabling Percy to reach France before them, but while Marguerite and Sir Andrew board the next ship they can find to Calais, it becomes clear that Cheuvalin is close behind them. The two reach a cafe in Calais that Percy is known to frequent, but Cheuvalin arrives there soon after, and Marguerite is forced to watch in hiding as Cheuvalin lays a trap for Percy. When Percy arrives, however, he manages to get the upper hand by switching Cheuvalin's snuff box with pepper, quickly slipping out after Cheuvalin is overcome by sneezing.
Cheuvalin's forces discover that Percy has hired a cart owned by a local Jewish businessman to take him to the secret place where Armand and the Pimpernel's latest rescuees are hiding. Cheuvalin hires the services of Benjamin Rosenbaum, another local Jewish businessman, to take him and his troops there as well, and Marguerite follows at a safe distance. She is quickly captured when she tries to warn the rescuees of the peril they are in, and Cheuvalin threatens her to remain quiet while the trap for Percy and the league is sprung. When it appears that Percy is close by, however, Marguerite is unable to remain quiet and desperately screams out a warning — only for it to be discovered that Percy is apparently nowhere present and the rescuees have already escaped to safety on Percy's private yacht. Cheuvalin learns that his men had seen the league escape but, warned by Cheuvalin not to interfere until Percy arrived on penalty of the strongest punishment, his men were paralysed into inaction because Percy was not present and ended up just watching them go.
Enraged and spiteful, Cheuvalin has both Marguerite and Benjamin tied up, and Benjamin viciously beaten by his men, before leaving them to lead the hunt for Percy, who is believed to be close by. Once he and his men have gone, however, Benjamin reveals that he is in fact Percy in disguise; having realised that his wife had accidentally betrayed him and knowing that Cheuvalin was on his trail, he decided to get close to Cheuvalin in order to warn the rest of the league under Cheuvalin's nose, banking that the ingrained French cultural prejudice towards to the Jewish people would mean that Cheuvalin would not examine his disguise too closely, and remained there once Marguerite was captured in order to ensure her safety. Injured after his severe beating, Marguerite helps Percy to the shore, where they are rescued by Armand and the crew of Percy's yacht. Marguerite and Percy forgive each other for their pride, distrust and mistakes towards each other, intentional or otherwise. Their relationship healed and their love for each other restored, Sir Percy and Marguerite live happily ever after, while Cheuvalin is never seen in polite British society after that point.