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.

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.

Vervain, now a slave, escapes and manages to find Hazel's warren. Vervain tells Woundwort and Campion is horrified. Campion sets off to warn Hazel, and is then amazed by the beauty of Watership Down when he sees it for himself. Hazel and his friends set traps for Woundwort's arrival. It is love at first sight for Blackberry and Campion. Now begins the final battle, and Fiver's scary vision becomes reality.

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.

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.

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.

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

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.

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.

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.

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.

Knowing Campion is still under arrest and Vervain is starving him to death, Hazel decides he must do something to help. The rabbits make a cunning plan to turn Vervain into a mad bunny! Afterwards Campion is soon up and running again.

Finally making it to the Big Water the rabbits lose contact with Kehaar. The rabbits are amazed by their new surroundings, including the salty sea water. The rabbits soon realize the sea is getting closer to them. Meanwhile, Kehaar meets up with his old friend, Katerina, but soon realizes that she isn't as friendly as he thought she once was. The rabbits are helped by the Puffins after almost being taken away by the sea.

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.

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.

Hickory and Marigold decide it's time to leave Cowslip's warren and set off to find Hazel. Hazel agrees to help them escape, and Hawkbit and Dandelion give them lessons on how to live outside in freedom. Hickory and Marigold decide to start a new warren. Concerned, Primrose suggests that they move into Redstone. Trouble is ahead of them though, when Hickory gets trapped on a roundabout.

Since the apples of the orchard are red and delicious Hazel and Bigwig go down to have a munch but retreat back to the warren when they find out a badger lives there. Knowing that the orchard is off-limits, Pipkin and Fiver go down to have a bite of the apples anyway. The badger comes back, and Pipkin flees. Fiver soon finds out the badger is harmless, and has a name: Bark.

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.

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.

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.

Hawkbit, Fiver, Pipkin and Dandelion raid the farm and to Hazel's surprise, they bring two other rabbits back to the down instead of food. Bluesky and Raincloud both say they are messengers from Prince Rainbow. Hazel catches on straight away that it's a scam, but he keeps quiet. The two demanding rabbits tell Pipkin they can fly, which leads into a lot of trouble.

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.

Kehaar becomes homesick of the Big Water and decides he must go and visit it, with the rabbits tagging along too. Smelling the glorious smell of carrots and lettuce, the rabbits wander inside a big farm van to nibble at the food. Suddenly the van drives off, and the rabbits find themselves at a market where they make friends with a pig.

Bigwig sets up an early morning Owsla patrol, but Hannah doesn't show up for her training. Later, she turns up with Hickory, excited that Hickory and Marigold have baby rabbits. Bigwig is annoyed with her and after an argument, Hannah leaves the down. Kehaar manages to convince Hannah to come to Redstone and she agrees. On her way to Redstone, she ends up stranded up a tree, and meets a Squirrel called Tassle.