Both Johnny Depp and Mia Wasikowska returns, with Sacha Baron Cohen joining the film.
Alice Kingsleigh has spent the past three years following in her father's footsteps and sailing the high seas. Upon her return to London from China, she finds out that her ex-fiancé, Hamish Ascot, has taken over his father's company and plans to have Alice sell him over her father's ship in exchange for her family home. Alice follows a butterfly she recognizes as Absolem and returns to Underland through a mirror.
Alice is greeted by the White Queen, the White Rabbit, the Tweedles, the Dormouse, the March Hare, Bayard, and the Cheshire Cat. They inform her that the Mad Hatter, Tarrant Hightopp is acting madder than usual in wake that he believes that his family is still alive. Alice tries to console him, but the Mad Hatter remains sure of his family's survival of the Attack of the Jabberwocky day.
Believing finding the Hatter's family is the only way to stop his deteriorating health, the White Queen decides for Alice to consult Time himself, and convince him to save the Hatter's family in the past (something that no Underland resident can do as it is said that history will be destroyed if someone sees their past/future self, while Alice has no past self in Underland for her to accidentally meet). Upon visiting Time's palace, Alice finds the Chronosphere, an object that powers all time in Underland.
After being told by Time that altering the past cannot be done, Alice steals the Chronosphere and travels back in time, shortly after finding the exiled Red Queen, Iracebeth of Crims, is in the care of Time. The Red Queen urges Time to go after Alice. Alice accidentally flies to the day of Iracebeth's coronation, where a younger Tarrant begins a mockery of the Red Queen when the royal crown doesn't fit on her abnormal head. This causes Iracebeth to melt down, and her father deems her inappropriate to rule, and passes the title of queen to her younger sister Mirana, the White Queen.
Alice later learns of an event in Iracebeth and Mirana's past that caused friction between the two, and she travels back in time again, hoping it will change Iracebeth's ways and cease the Jabberwocky from killing the Hatter's family. Mirana (as a young girl) steals a tart from her mother and eats it. When confronted by their mother, Mirana lies about eating the tart, and Iracebeth is accused, causing her to run out of the castle in sadness. Alice sees her about to run into a clock, the event that deforms her head and personality. She is able to get the clock out of the way, but fails to change the past as Iracabeth trips and slams her head anyway.
Alice is then confronted by a weakened Time, scolding her for putting all of time in danger. She runs into a nearby mirror back into the real world, where she wakes up in a mental hospital, diagnosed with female hysteria. With the help of her mother, she returns to Underland, where she travels to the Attack of the Jabberwocky and discovers that the Hatter's family never died, but were captured by Iracebeth. Returning to the present, Alice discovers she is too late, and that the Hatter is at the brink of death.
After Alice tearfully says that she believes him, Tarrant awakens and reforms back to his normal self. The Underlanders go to the Red Queen's castle, where Hatter finds his family shrunk and trapped in an ant farm. Iracebeth apprehends them and steals the Chronosphere from Alice, taking Mirana back to the day she lied about the tart. By the time Tarrant and Alice get there, Iracebeth and her past self see each other. Time becomes irrelevant, and Underland begins to freeze. Using the Chronosphere, Alice and the Hatter race back to the present, where Alice is able to place the Chronosphere back in its original place.
With the Chronosphere stabilized, Underland reverts to normal. The Hatter reunites with his family. Mirana apologizes to Iracebeth for lying, and both of them make amends. Alice bids her friends farewell and returns to the real world where her mother refuses to return Alice's ship over to Hamish, and the two set to travel the world together with their own company.
- Mia Wasikowska as Alice Kingsleigh
- Johnny Depp as Tarrant Hightopp, the Mad Hatter
- Helena Bonham Carter as Iracebeth of Crims, the Red Queen
- Anne Hathaway as Mirana of Marmoreal, the White Queen
- Sacha Baron Cohen as Time,a half-clock, half-human who has the ability to travel back and forth through different time periods with a special skill secreted in a gold-colored chromosphere.Todd says, "In terms of his behavior, he’s definitely the kookiest of all."
- Rhys Ifans as Zanik Hightopp, the Mad Hatter's father
- Matt Lucas as Tweedledee and Tweedledum
- Andrew Scott as Addison Bennet
- Ed Speleers as James Harcourt
- Michael Sheen as Nivens McTwisp, the White Rabbit
- Alan Rickman as Absolem, the Caterpillar
- Stephen Fry as Cheshire, the Cheshire Cat
- Timothy Spall as Bayard, the Bloodhound
- John Sessions as Humpty Dumpty
- Barbara Windsor as Mallymkun, the Dormouse
- Paul Whitehouse as Thackery Earwicket, the March Hare
- Bud Luckey as Uilleam, the Dodo Bird
- Toby Jones as Wilkins