Our Shmoop-patented, super-short summary: rabbits search for a safe home and eventually find it.
The slightly longer version is broken into four parts (just like the book itself):
Psychic rabbit Fiver has a bad feeling about his home, the Sandleford Warren (in England). But no one will listen to him except his big brother Hazel… and a few other rabbits, including a big rabbit named Bigwig.
So they leave and have some adventures, like crossing a river. The smart rabbit Blackberry invents a raft. The story-telling rabbit Dandelion tells a story about the mythological rabbit hero El-ahrairah. (So every rabbit has a role here, like in one of those heist movies where everyone's skill gets used to break into the casino. Although we don't remember a storyteller in that bunch.)
They meet some other rabbits led (sort of) by a fellow named Cowslip. These rabbits live in a warren that seems like paradise, despite what Fiver may tell you: no predators and lots of food. But it turns out that a farmer keeps this warren safe just so he can trap and kill a few rabbits now and again. (Isn't that always the way?) When Bigwig almost gets killed, the other rabbits decide that Fiver was actually a prophetic genius and not, in fact, nuts. So off they go to continue searching for their home.
Hazel's group of rabbits leaves the deadly warren and makes a new home on Watership Down, which doesn't have a lot of water and isn't a ship. (If you think about that too long, you'll go mad.) A rabbit named Holly who stayed behind in Sandleford comes to tell them that humans destroyed the warren after Hazel's group left, proving Fiver correct.
But now that they have a home, Hazel realizes they have no female rabbits, which is kind of a problem, since rabbits are all about the gettin' busy. Seriously, these things love them some procreating. They befriend a wounded seagull named Kehaar who flies around to find out where some other rabbits live. He finds (a) a nearby farm with some domesticated rabbits and (b) a nearby rabbit warren. All the single ladies say hey!
While some rabbits go to the warren to make friends ("can we have some of your women rabbits, please?"), Hazel raids the farm to free the rabbits there. And just because he wants to steal some rabbits, he gets shot by a human. Fiver saves Hazel, though he's permanently crippled. (Like Professor X in X-Men, but—you know—a rabbit.)
When the rabbits come back from the nearby warren (Efrafa), they report that Efrafa is organized like a prison or a totalitarian state. (Think Germany in World War II or Panem in The Hunger Games.) And the leader of Efrafa, General Woundwort, doesn't want to make friends or let any of his female rabbits go.
But Hazel still thinks Efrafa might be the best place to find a date. So he organizes a raid and plans to trick the Efrafans, especially their chief rabbit, Woundwort. Yeah, this has disaster written all over it.
Woundwort is a very scary, big rabbit—he's basically a bunny version of Hitler or Stalin or (fill in your favorite totalitarian leader here). But he's had some bad luck recently and needs some loyal officers. So when Bigwig comes to volunteer, Woundwort accepts him into the police force, because he's Big (word's still out on the wig thing).
Luckily for him, Bigwig meets a bunch of unhappy female rabbits who want to escape. So against all odds—and thanks to the seagull Kehaar who fights on their side—Hazel and Bigwig manage to escape with several female rabbits.
Now everything is perfect for the Watership Down Warren and they can live happily ever after.
Except for the fact that Woundwort wants to kill them all and is leading an army to attack.
And Woundwort would probably win—if it weren't for those meddling kids. No, wait, that's not right. He would probably win except that Hazel comes up with a crazy plan to lure a dog into attacking Woundwort's army.
And then they live happily ever after. Until Hazel dies peacefully in the epilogue and goes off to join the mythological hero El-ahrairah. So, yeah, there's very little "living happily ever after" in this book, but we think the warren is safe for many generations, thanks to Hazel.