Narrated by a small, loyal dog named Rebel, the story is set in a fictional country ruled by a tyrannical King whose guardsmen enforce heavy taxes, nighttime curfews, and a ban on dissent. Rebel lives on a sheep farm with 12-year-old Tom and Tom's Mum and Dad. Since Tom rescued him as a puppy from a snowy ditch, Rebel has never left the farm. His days are unchanging: waking Tom, sneaking breakfast scraps, tending sheep, and falling asleep beside Tom at night.
That routine shatters when two guardsmen, whom Rebel nicknames Rat and Slug, invade the farmhouse and demand double taxes. Tom protests, and Slug smashes every plate in the kitchen as punishment. Tom wants the family to resist, but Dad insists the Reds, a resistance movement defeated years earlier, cannot win against the King's army.
Soon after, a scarred stranger in a wolf's pelt appears at the fence of Top Field, the farm's upper pasture. He introduces himself as Rider and reveals a red neckerchief, identifying himself as a Red. Rider says thousands are preparing to march on the King's High Castle and that the Reds need Tom's charcoal drawings to inspire people. Tom lies about his age, claiming to be 16, and attends a secret meeting, ordering Rebel to stay.
Dad discovers the neckerchief in Tom's pocket, and Tom confesses he has sworn allegiance to the Reds. The next morning he apologizes and claims he burned it, but that afternoon he ties it around Rebel's neck, whispers "Stay," and walks into the forest with his knapsack. Mum finds a note: Tom has run away to join the uprising. The note includes a drawing of Tom atop the High Castle waving a red flag, and unlike every picture Tom has ever made, Rebel is not in it.
Priscilla, the farm cat, warns Rebel that Tom has joined a war and could die. Rebel decides that if Tom is his friend, not his master, he should stop obeying. He crawls under the fence, leaving the farm for the first time, and follows Tom's fading scent.
In Connick, a small market village, Tom's scent vanishes. A talkative pig named Seamus, caged on a wagon, explains that Rider hid the Reds in wagons heading to Drulter and mentions old sheep trails through the mountains that could get Rebel there faster. Rebel frees Seamus and heads for the trails.
On the mountain, Rebel eats sorrel, a plant poisonous to dogs, and collapses. He wakes beside Jaxon, a large dog who follows the code of the Masterless, dogs who reject human ownership and live in the wild. Jaxon reluctantly agrees to guide him. Along the way, Jaxon speaks of the Companion, an invisible spirit believed to walk beside every dog.
In Drulter, Rebel finds one of Tom's provocative drawings pinned to a tavern door. A pub dog named Rollo betrays them to the guardsmen Rat and Slug, who set fire to the gorse bushes where Rebel and Jaxon hide. Rebel bites Rat's leg when Rat aims his musket at Jaxon, causing a misfire. By the Masterless code, saving Jaxon's life binds Jaxon to a debt, and Rebel commands him toward Unsk, where the Reds and guardsmen are converging.
They are joined by Felix, a dormouse whose wife, Beatrice, was accidentally carried off in a bag of the Reds' weapons. Unsk has been devastated by battle, but Rebel discovers another of Tom's posters calling everyone to march on the High Castle. Tom is alive. Jaxon knows a shortcut through the wilderness.
The shortcut nearly kills them. Rebel saves Jaxon from drowning in a swollen river. When Jaxon injures his paw, a young shepherd girl named Pol carries him to a mountain hut she shares with her grandad, who treats the injury. Rebel notes how peaceful Jaxon seems, despite his insistence that human love costs dogs their freedom.
Once healed, they descend into a dead forest. Jaxon accuses Rebel of being too blind to see Tom has forgotten him. Rebel holds firm: Love means fighting for someone even if they do not ask. A starving wolf pack attacks. Jaxon fights the wolves while Rebel flees, but the pack leader chases Rebel to a cliff edge. Cornered, Rebel finds what Jaxon called his "True Dog," the wild, courageous core of himself, and lunges at the wolf. The collision sends them both over the cliff.
In a near-death vision, Rebel meets the Companion. The spirit leads him through scenes from his life to a golden cornfield stretching to an eternal horizon. The wolf bounds joyfully into it, but Rebel sees Tom and Jaxon behind him and refuses to follow. He wakes hanging from a tree branch, his neckerchief snagged during the fall.
Jaxon nurses Rebel for days. When Rebel recovers, he sees the High Castle just beyond a nearby ridge. Jaxon confesses he knew and begs Rebel to live free in the mountains with him instead. Rebel refuses, explaining that love "pins you to things" and compels you to act for others. They part.
Rebel reaches the gorge where the final battle rages. Thousands of Reds push toward the castle, but cannon fire breaks their charge. Rebel spots Tom wounded in a crater near the gates. He cannot save Tom but can ensure Tom is not alone. He sprints across the battlefield, his red neckerchief flying. The retreating Reds stop to watch. Rider sees the small dog, picks up his flag, and rallies the army. One by one, the Reds turn back. Rebel reaches Tom and leaps into his arms. The Reds surge forward and take the castle.
The King escapes through a secret tunnel, but his golden flag is replaced by a red one. In the hospital, Jaxon reappears, having followed Rebel into battle. As volunteers tend Tom, dozens of worn charcoal drawings spill from beneath his shirt: all pictures of Rebel. Tom has carried every sketch against his heart.
Rider tells Tom he has done enough and must go home. Tom confesses he never wanted to be a farmer. Rider encourages him to pursue his art, reminding Tom that the fighters were not trying to change the world but fighting for "the small nothings that make their days worthwhile." On the journey home, Rebel reunites Felix with Beatrice, who survived with newborn babies, and finds Seamus a new home as a pub pig.
In Connick, Rebel tells Jaxon he cannot come to the farm; keeping Jaxon there would be like caging a bird. He directs Jaxon to Pol and Grandad, where Jaxon can roam freely and return for warmth when he chooses. Jaxon sprints toward the mountains, tail wagging for the first time. Tom asks if Rebel wants to follow. Rebel runs to Tom without hesitation. The two walk side by side through the farm gate Rebel has never once passed through, and that is how he comes home.