In 1946 young Alec Ramsey and his father are traveling back to England on the steamship Drake passing the north coast of Africa. While out on deck, Alec sees a handsome black Arabian stallion being forced into its pen above decks by some cruel men, using a bullwhip to get the frightened animal into its quarters. Returning to his father's card game, Alec takes some sugar cubes from the coffee tray & brings them to the stall where the horse is tied up. Placing them on the railing of the door, Alec then hides from sight. Within minutes the animal has taken the cubes. As Alec turns around he is grabbed & roughly accosted by the mean-looking owner of the horse, who shouts menacingly in a foreign language before letting him go. Alec quickly returns to his cabin.
That night, Alec's father shows him his winnings from the card game. Alec receives a pocketknife and a small carving of a horse. His father tells him the horse is Bucephalus, the horse of Alexander the Great. Alec puts the Bucephalus carving on a shelf and falls asleep.
Later that night, the carving is illuminated with a bright orange light. The ship pitches violently and Alec is thrown from his bunk onto the cabin floor. Grabbing the carving & his pocketknife, Alec gets to his feet and his dad throws a lifejacket over him. As the two of them stagger out into the hall they discover frightened passengers fleeing their rooms. Alec's dad sees water pouring in through a door, and they make their way onto the deck. As Alec looks up he sees the superstructure of the ship blazing with fire. His dad leaves him below with instructions to hang on to a rail, and goes to the boat deck. As Alec stays put he hears the horse in its pen, and decides to set the animal free and give him his chance to fight for life. Fighting his way to the door, he gets it open, but is attacked again by the horse's owner who cuts the lifejacket from Alec's body with a knife. Seeing this, Alec's dad leaps onto the man from the upper deck & throws him against the rail. In seconds the man has disappeared. The horse breaks the ropes holding him in & charges out onto the deck.
Alec watches helplessly as the horse jumps the railing & into the water. A wave then washes over the ship, sending Alec backwards into the railing. Suddenly the railing gives way & Alec plummets into the water, helpless. Hearing the stallion and seeing its head above the water, its ropes caught in the propeller, Alec swims over & cuts the rope, freeing the stallion. He and the horse swim clear as the Drake, ablaze with fire, goes down by the head - taking everyone but Alec & the horse.
The following day Alec finds himself washed up on a remote island, apparently the only human survivor of the sinking of the Drake. Still carrying the Bucephalus carving & his knife, Alec starts trying to figure out how to survive. Finding a cave, he makes a fire and starts catching fish. He eventually discovers he is not alone - the horse has also survived, and is trapped with its ropes caught on some rocks. At first the frightened animal is wary of Alec, but he gets close enough to cut the ropes and free the horse, which shakes off the ropes & flees. Alec follows the horse's tracks, but they vanish in the sand.
Later, asleep on a beach, Alec is visited by an uninvited guest; an Asp Cobra. As Alec comes to he sees the reptile hissing, its hood spread, ready to strike. Alec, frozen with fear, tries to back away, but the snake hisses more aggressively. Suddenly, the horse appears, and pounds its sharp hooves on the cobra, killing the reptile. Again the horse vanishes as quickly as it appeared.
More and more, Alec begins to encounter the beautiful horse, and the two of them forge a strong bond, with Alec feeding the animal and bringing it fresh water, with the horse allowing Alec to ride him bareback. The bond between the boy & the horse becomes so entwined that when a rescue boat finds Alec, he refuses to leave without his beloved animal, and the horse refuses to let Alec go. The men on the rescue boat tether the horse and help the animal to a larger ship, and Alec & the horse - who he names 'The Black' - are on their way home to America.
Back home in the midwest U.S.A., Alec's mother is enormously relieved her son is alive but also grieving the loss of her husband, and expresses her thanks to The Black for saving Alec's life by allowing Alec to keep the horse in their backyard. Unfortunately, one day as the garbage collectors are coming round, a hat on the man's head triggers a fear in the Black's mind, and the animal is racing through the streets. Alec goes after the horse, and follows its trail to a barn owned by Henry Dailey - a former jockey & horse trainer. Alec inquires about learning to ride the Black, but Dailey is at first skeptical - no papers exist, and he's considered a wild stallion. However, Dailey agrees to teach Alec the ways of riding.
The two of them, along with the Black, undergo frequent, rigorous training in riding and saddling a horse. At first the Black is reluctant to allow a saddle but eventually becomes used to it, and soon Alec & the Black are making runs on a racetrack.
While at a movie theater, Alec sees an ad about an upcoming horse race, featuring two of the most famous horses & jockeys in the United States. Dailey gets in contact with a reporter who comes to watch Alec & The Black on the track one stormy night, and he writes a story on it - leading to a challenge match between The Black & the two Thoroughbreds. The Black is billed as a 'Mystery Horse' challenging the Thoroughbreds. Soon, promotions about the upcoming challenge are sprouting up everywhere, and even Alec's mother takes notice.
Eventually Alec reveals the truth to his mother; the Black is the 'Mystery Horse' challenging the others, and Alec will be riding him. At first Alec's mother refuses, fearing the worst after losing her husband. After talking with Henry and Alec again, though, Alec reveals the carving of Bucephalus and how he got it - and when. His mother relents & allows Alec to ride the Black in the challenge.
On race day, Alec suits up with Henry, and the other jockeys are stunned to find a rider half their size as their opponent. They smugly sneer that Alec won't be able to control a horse the size of the Black.
As they come out and prepare to enter the gates, one of the horses rears up and start kicking at the Black's feet. The Black defends himself, but it takes some effort to get the horses under control. The Black suffers a bloody wound to his lower front leg. The three horses finally make it into the starting gate.
Inside the starting gate, Alec looks down and sees the bloody wound to the Black's leg. As the gates open, Alec tries to restrain the Black, fearing that running would aggravate the wound. The Black is slowed, but after a few seconds shows Alec that he wants to race. Although far behind, the Black picks up speed and begins to close the gap on the other two horses. As the three horses exit the last turn and head down the home stretch, Alec and the Black pass the first horse - then the second - and seconds later Alec & the Black are across the finish line, triumphant. Alec waves his hands in the air & Henry and Alec's mother cheer wildly from the stands. The Black's leg is bandaged, and Alec & the Black proudly pose for the cameras with their winnings. The film ends showing Alec & the Black in their times alone, on the island.