Jenny returns from school and immediately angers the new neighor Armstrong by spoiling his fox hunt. A scruffy waif called Ned arrives at the Gordon's house and claims to be Amy's nephew. He refuses to follow the simplest of rules and tensions escalate with Armstrong.
Ned's behavior creates tension in the Gordon household and when items start disappearing, he is suspected. An older man Simey followed Ned from London and is threatening him to cooperate. It's up to Black Beauty and the children to help Ned.
Ned is caught in a lie by Dr. Gordon and decides to run away, encountering a drifter mistreating a circus pony. After Ned intervenes, the pony adopts him, leading to the man Rundle accusing him of theft. The misunderstandings escalate but are cleared up after Ned becomes a hero rescuing Squire Armstrong's daughter.
Briggs and his family are being evicted from one of the squire's cottages after his wife becomes ill. Dr. Gordon and his family become involved after Black Beauty is used in an escape while Jenny insists the Squire see the conditions his tenants live in.
Ned ignores Dr. Gordon's warning about keeping Jonah the pony away from yew leaves, which could poison him. When Jonah does indeed become sick, Dr. Gordon cannot leave John Danby's ailing wife, so it is up to Jenny, Ned, and Black Beauty to save the pony's life.
Mr. Joskins is selling quack remedies and Dr. Gordon intervenes after they make several of his patients ill. To get revenge Joskins tampers with Beauty's girth strap which injures Kevin while he is riding. Albert intially blames saddle maker Surtees but ultimately discovers the true villain.
While coming home late evening, Jenny and Ned catch glimpses of a mysterious figure in the shadows. Squire Armstrong again warns the Gordon household to stay away from his property but the children persist in investigating. A legend of an ancient treasure plays a part in the puzzle.
During a storm Squire Armstrong believes he was attacked by Black Beauty and promises if it happens again, Beauty will be destroyed. Jenny, Kevin, and Ned try to keep the horse contained but Beauty has a equine friend she must get to.
Charles Armstrong, the squire's nephew, arrives for a visit and soon quarrels with Albert and Ned. The boys are warned away from the sheep, who are about to lamb but one of them chooses not to during a race. Among the consequences is a struggle where Albert and Charles end up at the bottom of mine shaft.
There's been a drought causing a shortage of oats for Black Beauty. Ned works at the squire's stable to earn money for Aunt Amy's present, where he learns Potter is stealing oats and selling them secretly. Ned is not believed and Jenny is shut in a grain bin when they try to expose him. Beauty must come to the rescue.
Dr. Gordon and Black Beauty head to the quarry after a blast goes wrong and men are injured. Lawson is fired by the squire for negligence and in revenge he steals cash and horses, including Beauty. Beauty escapes, alerting Jenny and Kevin, who endanger themselves trying to stop Lawson.
Mr. Duncan, an old acquaintance of Dr. Gordon, asks for a letter of recommendation and is refused. Duncan vows revenge and hypnotizes Jenny to fear Black Beauty. Everyone is mystified until Albert starts to learn the truth.
Simey returns, seeking retribution on the Gordons for his time in prison. With his cohort Brit, they trick Ned, taking him and Black Beauty captive. Simey tries to sell Beauty to first Waggs, than at a market giving Ned a chance to escape.
Ned returns to the Gordons, having escaped from his abduction, but the constable doubts his story. Simey sells Beauty to Waggs but he escapes, attempting to return home. Beauty arrives at the Jones farm and is adopted by the young Rosie, who renames the horse Mike. Kevin, Ned and Jenny keep hoping for Black Beauty's return.
Squire Armstrong inherited a religious Indian idol from his grandfather and is outraged when it's stolen. Rana, a visitor to the community, is befriended by Jenny and Ned. He appears to have ties to the missing statue and Squire decides to act on his suspicions.
Ned spends his time playing circus with Jonah instead of doing chores, angering Dr. Gordon. Ned decides to run away when Alf and Wilt, two circus journeymen, ride through but they con him out of Jonah. Ned and the doctor need Black Beauty's help to get the pony back.
Albert takes Black Beauty for a run against Dr. Gordon's wishes and he forbids Kevin and Albert from riding the horse without permission. The boys have a falling out and Albert heads to the Grainger farm where he presents himself as an experienced trainer. He is tested when he gets on a dangerous stallion.
T. Otis Waygood and Dolly arrive in the village and Dolly, over Jenny's objections, borrows Beauty for a fast gallop. The squire is intrigued and sets up a match race between Jenny and Dolly. Ned recognizes the shady Waygood from his days in London and wonders what he's up to.
Paperwork is discovered revealing Black Beauty doesn't belong to the Gordons. The lawyer Crevache refuses to listen to reason so Jenny takes off with Beauty to keep him from being taken. In the end Black Beauty will decide who he should be with.
There are new inhabitants in the Eglinton manor with Kevin and Albert coming upon a young Cecily running away from her uncle. Joshua Eglinton claims to Dr. Gordon his niece has a nervous disposition and needs to be kept alone, but Kevin disobeys his father to rescue her. Albert dresses as Cecily allowing Kevin and Black Beauty time to save the young lady from her relative's nefarious intentions.
Ned is spending time with George downing trees while Jenny is excited about a party invite from Frances Bazely. Dr. Gordon asks Ned to escort Jenny but right before George is hurt by a fallen tree. Ned needs help from Beauty and Jenny to help his injured friend.
Kevin and Albert enjoy listening to the tales of Corporal Donovan, who claims to have been in the Light Brigade but Albert has his doubts. When men claiming to be the squire's employees evict Donovan, the boys come to his aid and with Beauty's help uncover stolen goods.
Dr. Gordon and Amy head to the city, leaving the youngsters on their own and arguing about who will ride Black Beauty. Albert sneaks off with Beauty to a carnival and loses the horse to shyster Teapot over a shill game debt. Kevin, Jenny, Ned, and Beauty must aid Albert in dealing with his blunder.
Mr. Coomb's dog is injured in one of the squire's traps and the older man doesn't know how he will watch his sheep. Dr. Gordon volunteers Kevin and Albert, who do their best but the sheep start mysteriously disappearing. Albert uncovers a rustling operation but needs Beauty's help to prove it.