Alice Cornwinkle is a working mother in New York City who's struggling to repair her marriage, be present for her child, and balance her career. Alice's husband, Jack, arrives to pick up their daughter, Chloe, for school as Alice rushes out the door for an important meeting. Chloe offers Alice her doll, Dinah, to bring with her for good luck. The three yearn to feel loved and at home again ("Home"). Alice arrives at work late, but just in time for a meeting where she is informed of an important assignment. Her company, Everheart Video Gaming Inc., is seeking a new CEO. She and fellow Senior Developer, Madelyn Quizzle, must each come up with a completely new video game concept centered around chess by the next morning to determine which of them will be the new CEO. Alice fights her insecurity and anxiety surrounding the assignment ("Worst Day of My Life").
Later that day, Alice sits at her desk working on her assignment and is determined to stay late to meet her deadline. She looks to Dinah, desperate for inspiration and sees a note in the doll's pocket and reads it aloud, putting herself to sleep. When she wakes up, her eyes meet with a rabbit. Rabbit grabs Dinah and leaves the room. Alice chases after Rabbit, following him down an alarmingly fast elevator and wondering if she's dreaming ("Down the Rabbit Hole").
Alice is transported to Club Wonderland. She catches a glimpse of Rabbit and follows him through the nightclub. Chaz, the club's DJ, steers the club-goers' attention to the celebrity in the room, Alice. The strange crowd welcomes Alice ("Welcome to Wonderland"). She finds Rabbit handing Dinah to a girl, who runs off with the doll. Alice confronts Rabbit and convinces him to lead her to find the girl. Rabbit takes her to a tiny door with a riddle. Alice reads it, perplexed, and is given a vial by a waiter. She drinks it and is shrunk to get through the door ("Drink Me").
Alice walks through the door to see a Caterpillar. She asks Caterpillar for advice on how to get out of Wonderland, but he speaks in riddles ("Advice from a Caterpillar"). Caterpillar gives her a pair of hugely oversized glasses to "see" the path. Frustrated, Alice begins to cry, which turns her back to her original size. The once oversized glasses now fit her, revealing a series of pathways. The path takes her to a lever. She pulls it and water rushes from all directions.
Alice encounters a boat full of cats, led by El Gato. El Gato reminds her to go with the flow, which will lead her both to the girl and the way out of Wonderland ("Go with the Flow"). Alice passes through a series of her memories with her childhood playthings. She experiences a flood of emotions as she's reminded of the side of herself that she's been neglecting: her inner child.
Suddenly, Rabbit appears again. Alice begs him to show her where the girl is. Rabbit gives Alice his backwards-running watch and introduces Alice to her White Knight. She reluctantly asks White Knight for help on her "quest" to find the girl ("One Knight"). White Knight gives Alice an all-access backstage pass to the Mad Tea Party ("The Mad Tea Party").
At the tea party, The Mad Hatter makes her grand entrance, expressing her plans to rule Wonderland ("The Mad Hatter"). The Mad Hatter decides to have everyone write what they don't like about Alice, put it in her hat, and read them one-by-one to get into Alice's head. The name-calling is stopped by the Queen's arrival. The Queen reminds her subjects of her royal power ("Hail the Queen"). She tells Alice that the only way she can leave Wonderland is to become Queen by winning a game at Squared Court and finding the lost girl.
As Alice heads on her way, Hatter also sets off to find the lost girl as a scheme against Alice. Hatter finds the girl, who reveals herself as Alice's younger self. Young Alice is convinced to journey with Hatter ("A Nice Little Walk"). Meanwhile, Rabbit tells Alice that Hatter has taken the girl to keep Alice away from the game. White Knight, El Gato, Rabbit, and Caterpillar all agree to help Alice to save her younger self from Hatter. Alice gives a pep talk to her team, and they set off for the Looking Glass Mirror to find Young Alice. Alice and her companions smash their way through the Looking Glass and begin their journey ("Through the Looking Glass").
Young Alice has been taken to Hatter's theme park. Hatter intends to wipe everyone's memories so she can take full control of Wonderland, beginning with Young Alice to make sure she wins at Squared Court and becomes Queen. The Hatter has also captured the heroes: White Knight, El Gato, and the Caterpillar ("Through The Looking Glass (Reprise)"). The Queen of Hearts seizes the heroes for smashing the Looking Glass mirror and declares their punishment ("Off With Their Heads").
Meanwhile, Rabbit and Alice approach a locked door and solve a puzzle to get through the door. Alice finds Chaz on the other side of the doorway. Chaz reminds Alice of the riddle from the door where she drank the potion. She realizes the riddle is about connecting with her "pure self": the younger version of her. Chaz reminds her that she needs to believe in her inner child to know who she truly is ("I Am My Own Invention"). Suddenly, Chaz is gone, and Young Alice appears. Alice embraces her, bringing back memories of love. They come together as one Alice ("Once More I Can See"). Rabbit finds Alice as two soldiers from Hatter's army appear. Alice manages to hide while they chase after Rabbit.
Back at the prison, White Knight, El Gato, Caterpillar, and Rabbit are moments away from execution. Disguised as part of Hatter's army, Alice bursts in alongside the knights. They fight Hatter's army, free the heroes, and break Hatter's brainwashing spell ("Together"). The Hatter reveals she is a part of Alice: her ambition and drive. She asks Alice to give in, join forces with her, and rule over Wonderland and the universe together. Alice refuses, creating the biggest earthquake yet, leaving the Queen no choice but to declare the game at Squared Court between Hatter and Alice to compete for the throne. Alice feels defeated; she doesn't think she can beat Hatter. White Knight reminds Alice of her strength, and they kiss ("Love Begins").
Alice and Hatter arrive at Squared Court ahead of the game. The Queen announces the rules of the game: whoever eliminates all their opponent's players wins. The game commences. Hatter and Alice battle, slowly eliminating each other's players. White Knight steps in to protect Alice and is stabbed by Hatter. Unknowingly, Alice and White Knight have landed on the Eighth Square. Alice has won ("I Will Prevail"). The Queen shares the riddle from her entrance to Wonderland with Alice once again. The riddle answers why Alice was sent to Wonderland: to realize that who she wants to be is who she is now. She has won the game and solved the riddle, so she can now leave Wonderland. Alice says her goodbyes and leaves ("Heroes").
Alice awakens from her dream the next morning. Worried that she wasn't home that night, Jack and Chloe came to the office. She apologizes to Jack and Chloe for not being herself lately, Jack apologizes as well for being selfish. They embrace and Alice invites them to stay for her big meeting. Alice decides she's going to propose a new genre of games that develop the heart, like what she experienced in Wonderland. She now sees the work through the eyes of her inner child ("Finding Wonderland").