Following the liberation (and destruction of Efrafa), the Efrafans move into Watership Down with Moss, the highest-ranking surviving officer, as their reluctant leader. Tensions are high as three of the other surviving officers try to bully Pipkin and end up getting into a fight with Bigwig. Meanwhile, Woundwort has survived and runs into two other rabbits in a swamp, letting them sink to their deaths in a mire after they refuse to swear loyalty to him. The Black Rabbit of Inlé shows this to Campion and tells him that his destiny is stop Woundwort, who "threatens the world of the living." Campion has a horrible vision of Blackberry in danger, and himself being threatened by a fierce green rabbit. Meanwhile, Moss and Heather decide to take the rest of the Efrafans to start a new warren elsewhere.

Vervain wanders about aimlessly, getting into all sorts of trouble. Bigwig, meanwhile, continues to push his Owsla. In the end Bigwig eventually accomplishes his goals and in doing so saves Vervain from getting into any more trouble.

The Junior Owsla and Kehaar help an orphaned Hawk survive, whilst at the same time trying to prove to Hazel they are responsible enough to go on solo patrol. What they don't know is that Hazel has been secretly watching them save the Hawk.

Undercover, Woundwort begins to gain the trust of the rabbits at Redstone Warren. He has to fight off his own allies in order to finally gain there trust. Meanwhile, Blackberry finds out about Campion.

Woundwort works his way to chieftainship of Redstone. Meanwhile, Kehaar decides to leave the warren for good with his new mate Gluck.

Woundwort discovers that a human construction crew plans to bulldoze Redstone. He and Vervain travel to the Warren of the Shining Wire where he tells Cowslip he will show him Redstone destroyed if Cowslip will give him his seer, Silverweed. Meanwhile, Hickory and Flax talk of revolt against "Weedstalk" while Marigold races to Watership Down to warn Hazel and the others of Woundwort's return. The wandering Campion stumbles across a new warren, Darkhaven, populated by savage rabbits who await the prophesized return of "the Dark One." He becomes their chief after he defeats their strongest warrior, Granite, winning the respect of a tough doe named Spartina.

Woundwort, Vervain, and Silverweed arrive at Darkhaven just in time to meet up with Campion. At the same time, Hannah learns magic so that she can help her friends.

Silverweed traps Fiver in a twisted dreamworld illusion, allowing him to invade Fiver's mind and see through his eyes to learn the location of Watership Down for his master, Woundwort. Fiver manages to fight off Silverweed's hold, but not before Silverweed deduces that Watership Down is "in the high hills, near a lone beech tree." Hazel realizes how dangerous Silverweed is so he and the others journey to Darkhaven with the intent of kidnapping him. Meanwhile, Campion and Blackberry have the same idea, whilst Granite becomes Woundwort's new second-in-command when he challenges Vervain to single combat. Vervain forfeits rather than face the stronger Granite.

Spartina is sent by Woundwort to befriend Hazel and the others and act as a spy for him. However Silverweed soon learns of her real objective. If Spartina does not return to Darkhaven by the next full moon, she has ordered Granite to kill Blackberry.

Spartina soon gets found out by the other Watership Down rabbits and she confesses everything, even admitting putting Blackberry in danger. After finding out about Spartina's betrayal, Woundwort uses her and Blackberry to make Campion confess where Watership Down is and to lead his army into battle there.

The Watership Down rabbits prepare for the last battle with Woundwort while Blackberry, Spartina and Campion plan their escape from Woundwort.

Primrose feels a little homesick for Redstone. Hazel agrees to take her back despite Fiver's warning that Redstone is empty. On the down, Fiver has another vision that one of their past enemies will return. Meanwhile, Hazel and Primrose are shocked to find that Fiver was right about Redstone being empty. The only one left there is Captain Broom.

Bigwig and Hazel worry about Watership Down being wiped out and that they have no idea of Woundwort's plans. Deciding that they will try to get Campion on their side they find him out on patrol and ask him to join up with them. Things seem to be going well, until Pipkin is taken away by the river after attempting to swim.

Wondering the burrow, Hawkbit discovers a strange chamber and believes he saw The Black Rabbit of Inlé. Concerned, Hawkbit goes to check it out again with Hazel and Fiver, but they encounter a cave-in. Bigwig believes Hazel, Fiver and Hawkbit have been kidnapped by Efrafa.

Hazel, having had new babies, decides to take a trip to the farm with Bigwig, Fiver, and Hawkbit in order to find food for the baby rabbits. Everything seems to be going well until they encounter a dog and a cat. Hannah gets herself into trouble too.

Free from Cowslip's warren, Strawberry begins to settle in at the down. Meanwhile, Bigwig hears of a vicious warren called Efrafa and investigates further.

Hazel travels to Nuthanger farm with Pipkin and Fiver to get some new hutch-rabbits to come and join them, in fear that if they don't have enough rabbits living with them they will be wiped out by Efrafa. Hazel heads for trouble involving a man and a gun. They bring back a new rabbit, called Clover.

Hazel, Bigwig, Fiver, Hawkbit and Blackberry all set off to help rescue Primrose and Blackavar from Efrafa. However, they get trapped under a stone bridge. Bigwig and Hazel have yet another argument and Bigwig storms off, forming a plan to rescue Blackavar and Primrose.

In search of Pimpernel, the rabbits travel to a nearby warren believed to be a place of safety. This warren, led by Cowslip, seems a little too good to be true...and it is!

After a huge storm, multiple sheep are at Watership Down. For now, Hazel agrees to let them stay. After living with them for a while, he soon finds out they aren't friendly and they attract more enemies. Captain Broom explains what a sheepdog can do to get rid of the sheep. Hazel hatches a cunning plan to get the sheep out of the down.

The Efrafan Owsla flee the collapsing caverns leaving only Woundwort, Vervain, Moss, and a handful of officers alive. Realizing that not even the cave-in will stop General Woundwort from trying to destroy them, Hazel, Fiver, and Bigwig make preparations to wage war on Efrafa with Pipkin recruiting all of his animal friends. Fiver meanwhile senses that Campion is not dead, and indeed the Efrafan captain manages to pull himself free from the rubble of the caverns alive but horribly scarred. He meets the Black Rabbit of Inlé, who tells him his time has not yet come and that he has a special destiny in store for him. Meanwhile Moss, seeing that Woundwort is going mad, teams up with a doe named Heather to overthrow him but the Watershippers attack Efrafa in full force.

The rabbits begin to settle into their new home on the down, however problems become apparent. The burrows need digging, but there's only one doe and bucks don't dig!! There's also a weasel that arrives at the down. Meanwhile, a mysterious visitor is looking for Bigwig.

Hazel, Fiver and Bigwig decide to take a visit to Efrafa after hearing reports that Efrafa want to kill all outsiders. Hazel encounters General Woundwort and asks him a few questions, unaware Woundwort is set out to kill him. While there, Hazel falls for a rabbit called Primrose. After Fiver has a vision about Woundwort's past they escape, making a new enemy in the process.

Bigwig joins Efrafa and plans to help Primrose escape. Meanwhile, Hazel and the others are still stuck under the stone bridge with the Efrafan guards on top of it. They hatch a plan with Kehaar and flee towards the grounds of Efrafa. They meet Bigwig there and he tells them of his plan to free Primrose and Blackavar. After some time, they finally elude the Efrafans and make their escape on a boat, leaving Woundwort raging.

Certain that the Efrafans are getting closer to the warren, Hazel and his friends decide to leave false trails leading them astray. However trouble lies for Captain Campion as he has an encounter with a Hawk. Hazel helps Campion but puts his own life in danger when they both meet an enemy the two of them have never encountered before.