Troubled by a strange recurring dream and mourning the loss of her beloved father (Marton Csokas), nineteen-year-old Alice Kingsleigh (Mia Wasikowska) attends a garden party at Lord Ascot's (Tim Piggott-Smith) estate, where she is confronted by an unwanted marriage proposal, to Hamish Ascot (Leo Bill), and the stifling expectations of the society in which she lives. Unsure of how to reply, and increasingly confused, she runs away to chase after a rabbit in a blue waistcoat, and accidentally falls into a large rabbit hole. She is transported to a world called Wonderland, where she is greeted by the White Rabbit (Michael Sheen), the Dormouse (Barbara Windsor), the Dodo (Michael Gough), the Tall Flowers (Imelda Staunton) and Tweedledum and Tweedledee (Matt Lucas in a dual role). They argue over her identity as "the right Alice", who it is foretold will slay the Red Queen's Jabberwocky (Christopher Lee) on the Frabjous Day and restore the White Queen to power as told by Absolem the Caterpillar (Alan Rickman). The group is then ambushed by the Bandersnatch and a group of playing-card soldiers led by the Knave of Hearts (Crispin Glover) capturing the White Rabbit and the Dodo bird. Alice, Tweedledum and Tweedledee escape and flee into the woods, while the Knave steals the Oraculum and the Dormouse leaves the others with the Bandersnatch's eye. Tweedledum and Tweedledee, however, were abducted by the Red Queen's Jubjub bird.
The Knave informs the Red Queen (Helena Bonham Carter) that Alice has returned and threatens her reign, and the soldiers and Bayard the Bloodhound (Timothy Spall) are ordered to find Alice immediately. Meanwhile, the wandering Alice encounters the Cheshire Cat (Stephen Fry), who takes her to the March Hare (Paul Whitehouse) and the Hatter (Johnny Depp). On the way to the White Queen's castle, Hatter relates the terror of the Red Queen's reign, and comments that Alice is not the same as she once was. The Hatter helps Alice avoid capture by allowing himself to be seized instead. Later, Alice is found by Bayard the Bloodhound (Timothy Spall), who wishes to take her to the White Queen (Anne Hathaway), but Alice insists upon helping the Hatter, so they go to the Red Queen's castle.
The Red Queen is unaware of Alice's true identity and therefore welcomes her as a guest. Alice learns that the Vorpal Sword (the only weapon capable of killing the Jabberwocky) is locked away in a case inside the Bandersnatch's den. The Knave crudely attempts to seduce Alice, but she rebuffs him. She later manages to retrieve the sword and befriend the Bandersnatch. The Knave finds her with the sword and attempts to arrest her. Alice escapes on the back of the Bandersnatch and delivers the sword to the White Queen (where she encounters Absolem again). The Cheshire Cat saves the Hatter from the executioner (Jim Carter), and the Hatter calls for rebellion against the Red Queen. The rebellion is quickly put down by the Jubjub bird. The resistance flees to the White Queen's castle, and both armies prepare for battle. Alice remains unsure about the expectation for her to champion the White Queen, and meets with a transforming Absolem. He reminds Alice of her past visit to Wonderland thirteen years earlier, and helps give her the courage to fight the Jabberwocky and accomplish "What she must to do", while he becomes a pupa.
When the Frabjous Day arrives, both the White and Red Queens gather their massive armies on a chessboard-like battlefield and send forth their chosen champions (armor-clad Alice and the Jabberwocky respectively) to decide the fate of Wonderland. As Alice fights the Jabberwocky, the White and Red Queen's armies start battling each other, with the Hatter dueling with the Knave and defeating him. Encouraging herself with the words of her late father, Alice manages to kill the Jabberwocky, ending the battle. The White Queen then banishes her evil elder sister and the Knave to the Outlands, and gives Alice a vial of the Jabberwocky's purple blood, which will take her home. The Hatter suggests that she could stay in Wonderland, but she decides that she must go back and promises that she will return.
Alice returns home, where she stands up to her family and pledges to live her life on her own terms. Impressed, Lord Ascot takes her in as his apprentice with the idea of establishing oceanic trade routes to China. As the story closes, Alice prepares to set off on a trading ship. Absolem, now a light blue butterfly, lands on her shoulder. Alice recognizes him and greets him before he flutters away.
