Following the Battle of Culloden the British army is triumphant over the rebel forces of Bonnie Prince Charlie. When the TARDIS arrives, the Doctor, Ben and Polly encounter fleeing Scots rebels and are taken prisoner by them. They all hide in a deserted cottage with the Laird Colin McLaren, who has been badly wounded, his daughter Kirsty, his piper Jamie McCrimmon and his son Alexander, who dies defending them from a patrol of English soldiers mopping up survivors. The patrol leader, Lt. Algernon Ffinch, is an ineffectual fop but his Sergeant is more forceful and takes the Doctor, Jamie, Ben, and the Laird to be hanged; while Polly and Kirsty manage to slip away.
The two women ending up hiding in a cave and then an animal pit to avoid Lt. Ffinch, who believes the Prince to be one of them following the rumour that he fled the battlefield as a woman. Eventually Ffinch finds them and they use their feminine wiles to entrap him and steal his money. Later in Inverness, the nearest major town to Culloden, they run into him again and use his previous foolishness to blackmail him.
Elsewhere on the battlefield the Royal Commissioner of Prisons, a shady character called Grey, has embarked on a scheme to enslave any highlanders still alive and ship them to the colonies. It is an illegal scam, but one he hopes will make him rich. He makes contact with an unscrupulous sea captain called Trask who agrees to put his ship, “The Annabelle”, to use in this end. Amongst the prisoners he identifies for sale are the Doctor, Jamie, Ben, and the Laird. They are taken to the prison in Inverness and incarcerated with many other prisoners, but the Doctor cons his way out of the drenched cell and then overpowers Grey and his secretary Perkins in order to make his escape. Grey is freed by Trask; and the captain reports that the transportation plan has begun and arranges that a number of prisoners, including Jamie, Ben and the Laird, are transferred to the ship. It is not long before the prisoners work out they could be being sold as slaves but most accept this fate, believing seven years indentured labour (a lie) is better than the gallows. Only Ben, Jamie, the Laird and one of his friends, Willie McKay, refuse to sign. When Ben attacks Grey, Trask has him thrown to the sea at the end of a rope.
The Doctor meanwhile has adopted the guise of a kitchen maid as well as a German and uses these identities to move freely around. He is reunited with Polly and Kirsty and, shortly afterward, Ben who has swum to safety. The Doctor boldly returns to Grey, having concocted a story about Bonnie Prince Charlie’s ring and him knowing the fugitive Prince’s whereabouts. Indeed, he names the prince as the piper Jamie. This is all a ruse to distract Grey and Trask while the girls free the prisoners from the hold and supply them with arms for an uprising. When Grey and Trask go examine Jamie in the hold they are captured by the armed highlanders and a revolt begins. Trask flees and ends up wounded and in the sea. Willie McKay takes control of the Annabelle and determines to sail her to freedom in France, happy to accept Perkins as a willing volunteer for this journey. Kirsty and her father are also passengers on the ship as it makes its bid for freedom.
The Doctor, Ben and Polly return to the town, using Grey as a hostage to ensure their safe passage around the area, and are joined by Jamie, who has decided to stay and help them find the TARDIS and therefore missing the boat to France with the his fellows. The party lose Grey but find Ffinch, whom they force to help them return to Culloden. But Grey has been clever: he reaches the cottage where he first met the Doctor, and brings with him a patrol of soldiers. Ffinch performs one last service – this one more purposefully without blackmail – when he arrests Grey for the transportation scheme. The solicitor has lost the paperwork (thanks to the Doctor) and is unable to prove any legality about his plans. Thanked by a kiss from Polly, Lt. Ffinch departs. The Doctor, Ben and Polly return to the TARDIS and invite their new friend, Jamie McCrimmon, on board. He nervously accepts.