The story begins in the spring, when a young male rabbit named Fiver has a vision and premonition that their rabbit warren in Sandleford will be destroyed. He and his older brother Hazel attempt to convince the Chief Rabbit to evacuate the warren, but their warning is not heeded. So they set off in the company of several other rabbits who either believe Fiver’s warning or are unhappy in their current roles. These rabbits include Bigwig, one of the Chief Rabbit’s Owsla officers and the largest and most physically imposing member of the group, a rabbit named Dandelion who is known as an excellent runner and storyteller, a rabbit named Blackberry who is unusually clever and who notices that wood floats on water.
From the moment they leave the warren, the rabbits are in constant danger. They are beset by enemies such as a dog in the forest, where they must escape by swimming and by pushing the weaker rabbits across on a makeshift raft, and rats that attack them when they spend the night in a barn. The rabbits’ adventures, and the way they bond with one another and eventually start to come together as a team and to acknowledge Hazel’s growing authority, is interpreted by many people as an allegory for a small military unit or for a group of refugees fleeing danger such as the Holocaust.
To provide some relief from the ongoing stress, Dandelion tells stories of El-Ahrairah, or the Prince with the Thousand Enemies. A folk hero and legend, El-Ahrairah is depicted at times as the king or ruler of all rabbits. Other characters in Dandelion’s stories include the Lord Frith, the creator of all the rabbits who is also identified with the sun, and the grim Black Rabbit of Inlé, who serves as a rabbit personification of death. Many of the stories contain morals or appeals to rabbit morality, which differs somewhat from human morality. Rabbits, for example, are urged to be fast, tricky, clever, and resourceful. There is no prohibition against theft, and rabbits are in fact encouraged and expected to steal vegetables out of farmers’ gardens. Yet there is also an expectation of honesty between rabbits and unity against elil, or predatory enemies.
At first the rabbits are traveling in search of a new warren. They find one that is mostly empty but that is populated by fat, healthy rabbits. This warren has no Chief Rabbit, but a rabbit named Cowslip welcomes Hazel and the other newcomers warmly. The Sandleford rabbits feel out of place in the new warren, where rabbits appear to have a taboo against asking questions, particularly ones that begin with the word “where”. The rabbits are fed regularly by a farmer who dumps large amounts of flayrah or high quality food for the rabbits to take. With such regular feeding, Hazel and the others cannot understand why the warren is not thriving especially since it shows no sign of recent disease. Even Strawberry, Hazel’s amiable host in the new warren, refuses to answer questions. Indeed, the rabbits in recite morbid poetry and press stones into walls to make pictures. The old stories of El-Ahrairah are not well received, and Fiver is extremely uncomfortable in the warren, which he says smells of death.
Cowslip and Strawberry’s warren is actually being used by the farmer as a kind of crop. It is set with snares every day so that the farmer can trap and kill rabbits regularly, perhaps for their meat or skins. The rabbits are fed well but are accustomed to having to go about above ground instead of grazing on the grass, So they frequently walk into snares. When a rabbit disappears, it is generally understood that he or she has been caught. Cowslip, Strawberry, and the rest of the rabbits in the warren decide to welcome Hazel and his travelers in the hope that they will be the next ones to be caught in snares, so as to allow the original rabbits to live a little bit longer. Hazel and the others do not discover the trap until Bigwig quarrels with Fiver and gets caught in a snare. Fiver and Pipkin (another small rabbit) succeed in biting through the wooden peg that holds the snare, freeing Bigwig. The Sandleford rabbits debate as to whether they should retaliate by attacking Cowslip and the others, but decide to leave instead. They are joined by Strawberry, who has just lost his mate to a snare and who completely repents of his role in the deception.
Many readers interpret Cowslip and Strawberry’s warren as an analogy for a despotic government or an institution that preys on its own people. The idea of trading personal security for luxury and losing their personal self-reliance in the process, which is what Cowslip and his peers do, has been used as a metaphor for slavery, for participation in an addicted or dysfunctional family, or for a suicide cult. The idea of rabbits collaborating voluntarily with humans seems bad and inappropriate to Hazel’s followers, who are used to regarding humans as dangerous predators.
Unbeknownst to Hazel and his group, the Sandleford warren is indeed destroyed by human beings who are clearing the land to build a real estate development. The humans plug up as many holes as they can find, pump poison gas down into the holes, and shoot the rabbits who escape through holes that are not plugged. There are only three survivors, two of whom make it past Cowslip and Strawberry’s warren to reunite with Hazel and his crew and to relate their story. The two survivors are Captain Holly, who was in charge of the Sandleford Owsla, and a jocular rabbit named Bluebell.
Hazel’s rabbits, with Strawberry, Bluebell, and Holly in tow, continue toward a high, lonely down—the Watership Down from which the book gets its name. They pass a farm and see things that are unfamiliar to Hazel, such as a road with vehicles passing. Upon arriving and climbing up to the top of the down, the rabbits realize they are home. They set about digging a new warren, but soon realize that all the rabbits who escaped from Sandleford are male. This is a problem, because without new generations of rabbits in a few years there will be no warren.
Hazel befriends an injured gull named Kehaar. He and Bigwig arrange to feed and shelter the gull until he heals, after which point Kehaar flies off in search of other rabbits. He finds four rabbits in a hutch on the farm: two bucks and two does. He also finds a large, well populated warren. So Hazel sends a group of rabbits out to investigate. Holly and a handful of other rabbits are sent as a diplomatic delegation to invite rabbits, particularly does, to move out of overpopulated runs and to join them on Watership Down.
Meanwhile, Hazel conducts a raid on the farm to free the hutch rabbits despite a warning from Fiver who says that Hazel, specifically, is in danger. The raid succeeds, and the team escapes with two does and one buck, but in the process Hazel is shot in the leg by one of the farmers. He escapes, crawling down a culvert, but is weak from blood loss. Fiver finds him and gets him back to the warren, where Kehaar removes the shotgun pellets, but the victory is bittersweet since Hazel remains lame in that leg.
Hazel returns to hear that the mission to the large warren (called Efrafa) has been a disaster. The warren is ruled by an aggressive and militaristic rabbit named General Woundwort who insists on a highly organized, militarized system wherein each rabbit is put into a group or Mark based on a scar given to them in their youth. Rabbits eat, sleep, and mate at times determined by their Mark, and any rabbit who tries to escape is caught and mutilated by the Owsla. General Woundwort is not at all interested in sending rabbits to Watership Down. In fact, Hazel’s emissaries are captured and impressed into the warren. They manage to escape, but the only reason they get away from the Efrafa patrol is because the pursuers are cut down by a train while crossing a railroad track at night.
Many readers compare Efrafa to a nation ruled by military dictators. All aspects of the residents’ lives are constrained, and many of the Efrafa rabbits are discontent and would be happier elsewhere. The rabbit Blackavar, who tried to escape, is forced to display his mutilated ears and describe how he is being punished, and how the Owsla was in fact merciful for not having simply killed him.
As Hazel recovers, the rabbits plot a way to get rabbits out of Efrafa. Bigwig goes undercover and joins the warren. He befriends a doe called Hyzenthlay who had been identified by Holly and the others as someone able to organize other does and to help them escape. Although one of the younger does is arrested and made to describe the details of the escape, Bigwig takes the does and Blackavar and runs for freedom during a thunderstorm. Kehaar attacks the pursuing rabbits, buying time for the rest of the rabbits to jump into a boat tied to a nearby bridge where Hazel is waiting, having bitten through the rope. The rabbits escape cleanly and return to Watership Down, and Kehaar flies away to his home near what he calls the Big Water. But the final reckoning remains.
Some months later, in the fall, General Woundwort’s patrols find Watership Down and the warren. They are seen by a field mouse who relays the story to Hazel, and the Watership Down rabbits prepare to fight. Hazel goes directly to General Woundwort with a proposal of an alliance between the two warrens, but is turned away. So the rabbits seal themselves underground, and Bigwig takes a position in the tunnel leading to where the rabbits and kittens are. Fiver collapses unconscious and is taken for dead by the invaders.
While Bigwig defends the run against General Woundwort himself, ambushing the larger rabbit and doing a great deal of damage, Hazel, Hyzenthlay, Blackberry and Dandelion return to the farm to release the farmers’ dog and lead it back to attack the Efrafa rabbits. The plan succeeds, and as General Woundwort withdraws from the attack after realizing Bigwig is not the warren’s Chief Rabbit, the Efrafa rabbits are attacked and driven off by the dog, which kills several of them.
The warren is saved, but Hazel is again injured and attacked by the farmer’s cat. The farmer’s daughter rescues Hazel and releases him later, where he rejoins his warren and lives to a ripe old age. In the end, the Black Rabbit comes for him but is revealed to be either El-Ahrairah or Lord Frith himself, and not a grim figure at all but a welcome and respected leader who invites Hazel to join his Owsla. Hazel agrees, leaves his body behind, and dashes away after his leader.