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 discovers that her ex-fiancé, Hamish Ascot, has taken over her father’s company and plans to have Alice sell him her father’s ship, “the Wonder”, in exchange for her family home. Unable to make a choice, Alice runs away, and comes across her butterfly friend Absolem, who disappears through a mysterious mirror in one of the upstairs rooms, returning to Underland.
There, Alice is greeted by Mirana of Marmoreal the White Queen, Nivens McTwisp the White Rabbit, the Tweedles, Mallymkun the Dormouse, Thackery Earwicket the March Hare, Bayard, and the Cheshire Cat. They inform her that Tarrant Hightopp the Mad Hatter is in poor health because his family is missing following the Attack of the Jabberwocky. The attack occurred shortly after his father, Zanik, a hat retailer, seemed to reject Tarrant’s gift of a hat creation.
The White Queen persuades Alice to convince Time himself to save the Mad Hatter’s family in the past, believing her to be the only one who can save the Hatter. However, she cautions Alice about time, and that if her past self sees her future self, everything will be history. As Alice sets out, she ends up in a dreary castle, where Time himself, a demigod that is part-human, part-clock, resides. As Alice tries to consult Time, she finds the Chronosphere, an object that powers all time in Underland and will allow her to travel to any time in the past.
Alice ignores Time’s warning that the past is unchangeable, and steals the Chronosphere, shortly after finding Iracebeth of Crims, the exiled Red Queen, in the care of Time. Alice accidentally flies to the day of Iracebeth’s coronation, where a younger Mad Hatter mocks the Red Queen when the royal crown doesn’t fit on her abnormally large head. This causes Iracebeth to melt down and her father deems her emotionally unqualified to rule and passes the title of queen to her younger sister, the White Queen.
Alice learns of an event in Iracebeth’s and Mirana’s past that caused friction between the two and travels back in time again, hoping it will change Iracebeth’s ways and stop the Jabberwocky from killing the Hatter’s family. She learns that the hat that the Mad Hatter thought his father threw away was actually treasured by him. Meanwhile, at the White Queen and the Red Queen’s castle, at the time they are children, Mirana 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. Alice sees that Iracebeth is about to run into a clock, thinking that’s the event that deforms her head and personality. Alice prevents that collision but fails to change the past, as Iracebeth trips and slams her head into a stone wall instead.