December 1860: After graduating from West Point, young Paul LeVal bids goodbye to his cousin Will Johnson and returns home to Lyon Ridge, South Carolina. However, in his absence, the resentment against the government’s interference in Southern affairs has developed into a burning rage, and soon after Paul’s return, South Carolina secedes from the Union. The other Southern states soon follow, joining with South Carolina to form a new country -- the Confederate States of America. By April 1861, both the Union and the Confederacy are preparing for war, and Paul and Will find themselves on opposite sides. Paul speaks out against the need for war, as he has always believed slavery to be an immoral institution; this would normally be grounds for a court martial, but Paul’s father is a friend of his commanding officer, and at his request, Paul is transferred to the command of Colonel Jubal Eustace, a man with a reputation for instilling discipline in his men. Sadly, as the war drags on, the situation in the South becomes dire, and in August 1863, a band of Confederate deserters attacks the LeVal homestead, seeking food. When Paul’s father tries to drive them off, they burn the house down with Paul’s parents trapped inside.

February 1865: The Doctor promises to show Peri some of her country’s past, but misses his target of the Wild West slightly. While Peri and Erimem dress for the period and collect a bag of gold coins from the TARDIS, the Doctor explores his surroundings -- and finds a Confederate officer and lieutenant preparing to burn down a farmhouse with a runaway slave and his family trapped inside. The Doctor creates a distraction and helps the slave and his family to escape, but in his haste to get away he is forced to leave Peri and Erimem behind. Peri is appalled when the officer, Colonel Eustace, psychotically beats his lieutenant for allowing the slaves to escape, and the lieutenant takes the beating with so much as flinching. Realising how much danger the dark-skinned Erimem is in, Peri puts on a southern accent and tells Eustace that she and her slave were attacked by Union soldiers who stole all of their possessions. Eustace escorts them (or rather, Peri) to a nearby village, Buckley, Virginia, where Peri rents rooms from the dour old Hilary Makepeace. Hilary believes that taking in boarders is beneath her, but she has fallen on hard times and has little choice; nevertheless, she is particularly upset about having to shelter Erimem, and only changes her tune when Peri pays her with the gold coins from the TARDIS. Unfortunately, Eustace also notes the gold, and sets his sights on courting Peri and acquiring her fortune.

The Doctor and the escaped slave, Moses Smith, reach safety with the help of Captain Will Johnson -- who catches a glimpse of Eustace’s lieutenant and recognises him as Paul. Unable to help his cousin, he escorts the Doctor and Moses to Gable, West Virginia, but must restrain the Doctor from riding straight back into danger to help his friends. The Doctor reluctantly agrees to pitch in at the army barracks, hoping that Peri knows enough of this time period to keep herself and Erimem safe. In the meantime, he attends to medical duties in Gable, and is present when the Union army liberates the prison at Billingate. Moses Smith volunteers to join the Union army, and is placed under Will’s command. Will writes regular letters home to his sweetheart, Claire, keeping her informed of these developments.

Peri fends off Eustace’s unwanted advances by claiming to have a fiancé, Doctor John Smith, but Eustace barely controls his rage at this news -- and when Erimem innocently bursts in on him and Peri unannounced, he nearly shoots her dead. Peri saves her friend by slapping her and ordering her back to her room; fortunately, Erimem, shaken by her close call, recognises that Eustace is quite mad and understands why Peri did what she did. Erimem and Peri quietly make preparations to flee to Richmond, while Eustace sends an urgent request for information to Captain Jackson Price regarding a certain Dr. John Smith. By the end of March, Peri and Erimem are ready to go -- but Eustace receives word that a man named Dr. John Smith has been sighted helping the Union forces at Billingsgate. Eustace confronts Peri with this information, but Erimem saves her friend’s life by striking Eustace down with a poker. Peri and Erimem flee to Richmond, but Eustace recovers and follows them after burning down Hilary Makepeace’s home in a fit of rage. Hilary cannot believe that a Southern gentleman could be capable of such an act, and presumably goes to her grave still convinced that Peri and Erimem were responsible.

The Doctor, Will and Moses also make their way to Richmond, where they contact Cassius Eldon, a former slave and member of the Underground Railroad. He promises to keep an eye out for Peri and Erimem, but Will then receives word that President Lincoln has arrived in Richmond, has missed his military escort, and is now walking through the streets, surrounded by adoring crowds of former slaves but without protection. Torn between his duty to his friends and his duty to history, the Doctor accompanies Will and Moses, and intervenes just in time to prevent a Confederate soldier named Aaron Eddowes from shooting the President down in the street. The angry mob is about to turn on Eddowes, but Lincoln intervenes, saving the life of the man who tried to kill him.

Moses escorts Eddowes to the jailhouse, while the Doctor and Will escort Lincoln to the home of former Confederate President Jeff Davis. Despite the apparently happy occasion, Will notices that the Doctor seems saddened while listening to Lincoln’s enthusiastic plans for the future. Moses then returns and reports having glimpsed a white and black woman together in the crowd; he was unable to confirm their identity until he’d dropped off Eddowes, but has since learned that they are indeed the Doctor’s friends -- and that Eustace has arrived in Richmond, in hot pursuit.

Peri and Erimem arrive at Eldon’s home, where they meet two former slaves -- the elderly George and the teenage Michael -- and learn that the Doctor is in town. Before they can set off after him, however, Eustace and his lieutenant arrive. Eustace shoots and injures Michael, kills George when George tries to pull a gun on him, and then strikes Peri down and prepares to shoot Erimem as she watches. At the last moment, the Doctor arrives, and Eustace becomes enraged when the Doctor refers to the dark-skinned Erimem as his friend and shows no fear of Eustace. While Eustace is distracted, Moses and Will enter the barn and get the drop on him. Eustace orders his lieutenant to shoot them, but as Will believed, this is Paul LeVal, and even after all the horrors he’s seen, he can’t bring himself to shoot his cousin.

Enraged, Eustace shoots Moses before anyone realises what he’s doing, but as he turns his gun on Erimem, the dazed Peri picks up George’s gun and shoots Eustace. She meant only to wound him, but the bullet strikes him in the head, killing him. Paul empties his own gun into Eustace’s body and collapses, his spirit broken. Will has Paul and the concussed Peri taken to a hotel, and when the Doctor tends their injuries he finds that Paul has been beaten repeatedly and has a gangrenous infection in his leg. Though Peri recovers fairly quickly from her concussion, she remains traumatised at having committed murder, and finds herself unable to speak to Erimem.