Alice Kingsleigh has spent the past three years following her father's footsteps and sailing the
high seas. Upon her return to London from China, she learns that her ex-fiancé, Hamish Ascot,
has taken over his deceased father's company and plans to have Alice sign over her father's ship
in exchange for her family home. Alice follows a butterfly she recognizes as the Absolem the
Butterfly, who was previously a caterpillar, and returns to Wonderland through a mirror. Alice is
greeted by the White Queen, the White Rabbit, the Tweedles, the Dormouse, the March Hare,
the Bloodhound and the Cheshire Cat. They inform her that the Mad Hatter is acting madder than
usual because his family is missing.
Alice tries to console him, but he remains certain that his family survived the attack of the
Jabberwocky. The White Queen, believing that finding the Hatter's family is the only way to
restore his health, sends Alice to consult Time and convince him to save the Hatter's family in the
past. The White Queen warns Alice that history will be destroyed if a person's past and present
selves meet. Upon entering the Castle of Eternity, Alice finds the Chronosphere, an object that
controls all of time in Wonderland. After Time tells Alice that altering the past is impossible, she
steals the Chronosphere and travels back in time, shortly after finding the exiled Red Queen in
Time's care. The Red Queen orders Time to pursue Alice, who accidentally travels to the Red
Queen's coronation. There, a younger Mad Hatter mocks the Red Queen when the royal crown
does not fit her abnormal head. When her crown breaks, the Red Queen throws a tantrum that
causes her head to swell. Her father deems her unfit to rule and passes the title of queen to her
younger sister, the White Queen.
Alice learns of an event in both the Queens' pasts that causes friction between the two, and she
travels back in time again, hoping to change the Red Queen's character and stop the
Jabberwocky from killing the Hatter's family. The young White Queen steals a tart from her
mother and eats it. When confronted by their mother, she lies about eating the tart, which gets
her sister accused and causes her to run out of the castle in a fit. Alice sees her about to run into
a clock and believes this to be the event that deforms her head and personality. She manages to
move the clock out of the way, but fails to change the past as the Red Queen actually stumbles
and hits her head. Alice is confronted by a weakened Time, who berates 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
Wonderland, where she travels to the Jabberwocky attack and discovers that the Hatter's family
did not die, but were captured by the Red Queen's Red Knights.
Returning to the present, Alice discovers the Mad Hatter at the brink of death. After Alice tearfully
says that she believes him, the Hatter awakens and reforms back to his normal self. The
Wonderlanders go to the Red Queen's castle and find the Hatter's family shrunk and trapped in
an ant farm. The Red Queen apprehends them and steals the Chronosphere from Alice, taking
her sister back to the day she lied about the tart. By the time Alice and Hatter get there, the Red
Queen and her past self see each other. This creates a time paradox, and Wonderland quickly
turns to rust. 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,
Wonderland reverts to normal. The Mad Hatter reunites with his family. The White Queen
apologizes to her sister for lying, and both of them make amends. Alice bids her friends farewell
and returns to the real world where her mother refuses to turn Alice's ship over to Hamish, and
the two set to travel the world on behalf of their own company.