Part 1: The Journey
The real Watership Down, near the Hampshire village of Kingsclere, in 1975In the Sandleford warren, Fiver, a runt buck rabbit who is a seer, receives a frightening vision of his warren's imminent destruction.[22][b] He and his brother Hazel fail to convince the Threarah, their Chief Rabbit, of the need to evacuate; they then try to convince the other rabbits, but only succeed in gaining nine followers, all bucks. Captain Holly of the Sandleford Owsla (the warren's military caste) accuses the group of fomenting dissension against the Threarah and tries to stop them from leaving, but is driven off.
Once out in the world, the traveling group of rabbits finds itself following the leadership of Hazel, who had been considered an unimportant member of the warren. The group travels far through dangerous territory. Bigwig and Silver, both former Owsla and the strongest rabbits among them, protect the others, helped by the ingenuity of Blackberry (the cleverest rabbit) and Hazel's good judgement. Along the way, they cross the River Enborne, and evade a badger, a dog, a crow, and a car. Hazel and Bigwig also stop three rabbits from attempting to return to the Sandleford warren.
A rabbit named Cowslip invites Hazel's group to join his warren, where a farmer leaves food for the rabbits and shoots all the predators. Fiver senses death and deception in the new warren, but the rest of Hazel's group, enjoying the peace and good food, decide to ignore Fiver's warnings and the strange and evasive behaviour of the new rabbits. Later, Bigwig is caught in a snare, only surviving the ordeal thanks to Blackberry and Hazel's quick thinking. Fiver deduces the truth, and admonishes the rest in a wild lecture; the farmer feeds and protects the rabbits so he can harvest them for meat and skins, and Cowslip's rabbits only invited the guests into their warren to increase their own odds of survival. The Sandleford rabbits, badly shaken, continue on their journey. They are joined by Strawberry, a buck who deserts Cowslip's warren.
Part 2: On Watership Down
Nuthanger Farm, Hampshire, England, in 2004Fiver's visions instruct the rabbits to seek a home atop the hills. The group eventually finds and settles in a beech hanger (a wooded hill) on Watership Down. While digging the new warren, they are joined by Captain Holly and his friend Bluebell. Holly is severely wounded, and both rabbits are ill from exhaustion, having escaped both the violent destruction of the Sandleford Warren by humans and an attack by Cowslip's rabbits along the way. Holly's ordeal has left him a changed rabbit, and, after telling the others that Fiver's terrible vision has come true, he offers to join Hazel's band in whatever way they will have him.
Although Watership Down is a peaceful habitat, Hazel realizes that, with all buck rabbits and no does, the warren will soon die out. With the help of their useful new friend, a black-headed gull named Kehaar, they discover a nearby warren called Efrafa, which is overcrowded. At Hazel's request, Holly leads a small embassy to Efrafa to present their request for does.
Hazel and Pipkin (the smallest rabbit) decide to scout out the nearby Nuthanger Farm, where they find a rabbit hutch. Despite their uncertainty about living wild, the four hutch rabbits are willing to come to Watership. Two nights later, Hazel leads a raid on the farm, which frees two does and a buck from the hutch. Hazel is wounded in the leg by the farmer's shotgun and presumed dead; Fiver's visions prompt him and Blackberry to return and rescue Hazel. When the embassy to Efrafa returns soon after, Hazel and his rabbits learn that Efrafa is a police state run by the ferocious despot General Woundwort, who refuses to allow anyone to leave his warren. Holly and his three companions have managed to escape with little more than their lives.
Part 3: Efrafa
While they were imprisoned in Efrafa, Holly's group had met an Efrafan doe named Hyzenthlay, who wishes to leave the warren and can recruit other does to join in the escape. Hazel and Blackberry devise a plan to rescue Hyzenthlay's group and bring them to Watership Down.
Bigwig infiltrates Efrafa in the guise of a 'hlessi' (a wandering rabbit unattached to any warren). He is recruited into the Efrafan Owsla by Woundwort, while Hazel and several other Watership rabbits hide across the nearby River Test. With help from Kehaar, Bigwig manages to free Hyzenthlay and nine other does, as well as a condemned Efrafan prisoner named Blackavar. Woundwort and his officers pursue them, but the Watership rabbits and the escapees use a punt to float away down the Test and escape.
Part 4: Hazel-rah
Downriver, the punt strikes a bridge, killing one doe. Once the rabbits are back on shore, they begin the long journey home, losing one more doe to a fox along the way. As they near Watership, they come across Captain Campion and his Efrafan patrol, who have been tracking them. Blackavar advises Hazel that the patrol must be killed to prevent them from reporting to Woundwort, but Hazel spares them and sends them off.
A few weeks later, the Owsla of Efrafa, led by Woundwort, unexpectedly arrives to destroy the warren at Watership Down and take back the escapees. Fiver experiences another vision, which gives Hazel the solution to the problem. While Bigwig fights and injures Woundwort in a narrow tunnel, preventing the rest of the Efrafans from getting any further into the burrows, Hazel, Dandelion and Blackberry return to Nuthanger Farm. They release Bob, the farmer's Labrador, and lure him back to Watership Down. Bob attacks the Efrafans, who flee in terror, leaving Woundwort to stubbornly stand his ground unobserved. Woundwort's body is never found, and Groundsel, one of his former officers, continues to fervently believe the General survived.
After releasing the dog, Hazel is attacked by one of the farmhouse cats. He is saved by young Lucy, the former owner of the escaped hutch rabbits. Upon returning to Watership, Hazel effects a lasting peace and friendship between the remaining Efrafans and the Watership rabbits. Some time later, Hazel and Campion, the intelligent new chief of Efrafa, send rabbits to start a new warren at Caesar's Belt, to relieve the effects of overcrowding at both their warrens.
Epilogue
As time goes on, the three warrens on the downs prosper under Hazel, Campion and Groundsel (their respective chiefs). Woundwort never returns; he becomes a legend among the rabbits, and a sort of bogeyman to frighten rabbit kits. Kehaar rejoins his colony, but continues to visit the rabbits every winter. He refuses to search for Woundwort, showing that even he still fears him.
Years later, on a cold March morning, an elderly Hazel is visited by El-ahrairah, the legendary rabbit folk hero and spiritual Prince of the Rabbits. He invites Hazel to join his Owsla, reassuring Hazel of Watership's future success and prosperity. Leaving his friends and his physical body behind, Hazel departs Watership Down with El-ahrairah.