After Annie's wedding, life returns to normal and they ignore Lorna's summons to London. Then, when John returns from being at a wrestling match, he finds Lorna gone. While he was away , men from the King's court arrived and insisted that she return with them to London. Lorna has left him a letter in which she explains that her great uncle, who is a powerful lord, is her guardian until she's 21, and she must live under his care. She had pleaded with the messengers to leave her at Plover's Barrows, but they had their orders. Jeremy Stickles, who is now up and about, has also received orders from the Court to send her to London. Lorna concludes her letter by telling John never to doubt her love for him.
Months go by and, mourning the loss of Lorna, John goes to visit Annie and pour out his woes, then goes on to see Reuben and Ruth. Ben is a bit sour, not having forgiven John for refusing to help with the mine. Ruth, however, listens sympathetically to his story and despite her own hurt advises John to follow Lorna to London and woo her. The farm work must be done, though, heartbreak notwithstanding, and John is soon busy bringing in the harvest. At first they worry that the Doones will retaliate and burn the farm, but it turns out they are too busy fortifying their defenses, assuming the government will be sending more- and better- troops. This probably would have happened, but King Charles suddenly dies, throwing the country into turmoil.
The Doones, having been quiet since the rebellion, when six of them were caught and hanged for supporting Monmouth, are now returning to their habitual villainy. On one of their raids, they abduct two respectable young girls, which upsets the community. Then worse happens: the Doones attack the home of a local farmer who is away, carrying off his wife and killing his infant son for "fun". This is the final straw, and the people of the community rally around John, looking to him for leadership. He doesn't want to lead them, and tells them to go to the magistrates, but the people know that they are useless. They convince John to go to the Doones and demand that Mistress Margery be returned, and the man who killed the baby turned over to them. Reluctantly, John goes to Doone Valley under a flag of truce and meets with Carver. Carver sneeringly rejects the idea of the Doones being held to the same standards as ordinary men, or that they should be punished for their " youthful frolic". Not only does he refuse John's terms, he orders his men to kill him, and they start shooting. John manages to escape, but the die is cast- they will attack the Doones.
To make John's happiness complete, soon after this Lorna returns. Her guardian has died, and she successfully petitioned the King to allow her to return to Exmoor. Unwilling to wait any longer, they quickly organize their wedding, with help from John's mother and sisters, and even Ruth Huckaback, who is persuaded to come. In their local church, surrounded by family and friends, the happy couple are wed. Just as they finish their vows, however, a shot rings out and Lorna falls into John's arms. Carver Doone has entered the church unseen and shot her.
John takes Ensie and rides back home, weakened from blood loss and grief. Thanks to Ruth, however, Lorna is still alive. Despite the doctor having declared her dead, Ruth works on Lorna, removing the bullet and cleaning and bandaging the wound herself. Lorna begins to come around, and Ruth cares for her day in and day out until she recovers. Indeed, she ends up healing faster than John, because while Ruth is busy taking care of Lorna, John is left to the tender mercies of the doctor, who is an idiot. He nearly kills John with blood loss by bleeding him constantly before a horrified Ruth realizes what's going on and puts a stop to it.
In the end, all is well. John and Lorna are reunited, and settle happily on the farm, saving most of Lorna's money as an inheritance for their children. Tom Faggus, with help from Jeremy Stickles, obtains a new pardon and settles down with Annie to raise their family, and Lizzie ends up marrying the Captain of the guards who was stationed at Plover's Barrows during their trouble with the Doones. Ruth remains single, inheriting Reuben's wealth when he dies, but John relates that there is a worthy local man who has fallen in love with her, and whom he thinks will eventually win her hand. John sends Ensie to school, and though he is heir to the Doone lands and title, he does not claim them, or even go by the name Doone, as he thinks of John as his father.