Two young rabbits, Hazel and Fiver, are out feeding. Though they are each only a year old and still under their full weight, it is clear that Hazel will be a large rabbit but that Fiver will never be large. Fiver begins to get a bad feeling about the area. When they stumble upon a sign planted into the ground nearby, he falls into a panic, telling Hazel that something terrible is coming to the warren. The sign that the rabbits could not read describes the housing development that is soon to be built right on top of their warren.
Fiver has a nightmare that something terrible will happen to the warren, and he convinces Hazel that they must go visit the Chief Rabbit. Hazel convinces a member of the Owsla (the leading rabbits who surround the Chief Rabbit) named Bigwig to let them see the Chief Rabbit. Hazel tells him that Fiver is his brother, and Fiver tells the Chief Rabbit, called the Threarah (rah is added to the name of a leader), of his premonition. However, the Threarah ignores the warning and yells at Bigwig for letting them interrupt his sleep.
Hazel, Fiver, and two of their friends, Dandelion and Blackberry, are discussing the conversation with the Chief Rabbit when Bigwig comes up to the group. He has left the Owsla and wants to leave the warren with them. Hazel says that they will leave that evening, at moonrise, and that they should try to convince other rabbits to come.
Hazel, Fiver, and Pipkin (a friend of Fiver's) wait for the other rabbits to arrive. Dandelion gets Hawkbit to come, and Blackberry brings Buckthorn, a large rabbit likely to soon be a member of the Owsla, and two other rabbits Hazel does not know, Acorn and Speedwell. They wait a while, and finally Bigwig comes with Silver, a large rabbit who recently joined the Owsla. Just before they leave, Captain Holly, leader of the Owsla, comes to arrest Bigwig because he believes they want to overthrow the Chief Rabbit. Bigwig attacks Holly and forces him to retreat. The rabbits leave.
The rabbits spend the night crawling through the woods, slowly and cautiously. Hazel leads them forward, going forward himself at times to make sure the way is safe. The rabbits grow exhausted, however, and they decide to rest. Hazel realizes they are tense and nervous, so he asks Dandelion to tell them a story.
Dandelion tells a story about El-ahrairah, the rabbit folk hero. The story goes that when the world was first made, all of the animals were friends and the rabbits populated the entire earth. But then Frith, the sun god who created the world, told El-ahrairah to stop his people from multiplying. Frith decided to trick El-ahrairah, and he told all of the animals to come get a gift. To foxes, stoats, weasels, and many other animals Frith gave gifts of cunning and strength to hunt rabbits. El-ahrairah heard this and decided to hide from Frith. He began to dig a hole, but at that moment Frith came upon him. Frith told the prince of the rabbits that he would have a thousand enemies, but that they would have to catch him, and that if his people were crafty they would survive.
A lendri (badger) surprises the rabbits and they run away from it. Then they come to a river that Fiver decides they need to cross, but they are unsure if they can. To the rabbits the river seems immense, but on the other side are fields that look much better than they woods where they have been.
It is clear from the beginning that Fiver is correct in his premonition that something bad will happen to the warren. However, the chain of events that occurs after Hazel and Fiver speak to the Threarah in some ways seems inevitable. A young rabbit comes to the Chief Rabbit claiming that they must leave their warren and move somewhere else. The Chief Rabbit is not willing to entertain this sort of suggestion, and he has good reason. Moving the warren would be a very difficult task, and it would also upset the balance of power. The Chief Rabbit is already the highest-ranking rabbit, so he has little to gain if he takes Fiver's advice. But while the Threarah can only lose if the rabbits leave the warren, young rabbits like Hazel and Fiver have much to gain. Unfortunately, Fiver's advice might easily be interpreted as an attempt to gain power. Personal reward is seen as the primary motivating factor for rabbits' actions—a strong parallel between rabbit and human societies. The Threarah and his Owsla would not be entirely incorrect with this view, as Fiver, Hazel, and the other rabbits are unhappy with the warren. They do not convince anyone to leave who is not already discontented. Rabbit society, like human society and perhaps all societies, is made up of some individuals who have advantages and are happy, and others who are disadvantaged and upset.
Captain Holly tries to stop Hazel and the others because he believes that they are in the process of staging a coup. His act demonstrates the actions of rabbits in power: they judge others' actions according to how those acts might affect their own power, and if there is a possibility of a threat, they react in order to protect their position. Although Bigwig leaves the Owsla and takes Silver with him because he wants to leave with Hazel, Holly sees the defection of two of the leading rabbits and assumes they must be plotting something. Bigwig leaves the Owsla because he does not consider their powers and privileges to be anything special and because he believes Fiver. However, Holly and the other Owsla members cannot understand that. They themselves want those powers and privileges, so they cannot comprehend why anyone else would willingly give them up. Therefore, they reason that Bigwig is attempting to arrange a coup in order to get even more power for himself. Hazel and his friends, leaving because they trust Fiver but also because they are unhappy at the warren, want to find a better life somewhere else. Bigwig and Silver also want a better life, even though they are in positions of authority at the warren. Bigwig and Silver hold different concepts of happiness than the other Owsla; because of this, they must force their way out of the warren, even though they mean no harm.