Alice's tales of her adventures in Wonderland result in her father committing her to a mental asylum where she was about to be lobotomised to cure her supposed insanity, but the Knave of Hearts and the White Rabbit rescue her and bring her back to Wonderland when they reveal that her true love Cyrus is still alive. As Alice begins a quest to find him, the Red Queen and Jafar plot against her.

A flashback reveals Cyrus' origin; Alice wants answers from the White Rabbit; disdain between the Red Queen and Jafar comes to a head.

The all-powerful Jafar succeeds in making his father love him and forcing Anastasia into thinking she loves him. After Alice, Amara and Cyrus escape, Jafar imprisons the Jabberwocky and calls upon an army of dead soldiers to do his bidding. Meanwhile, Alice and the White Rabbit raise their own army to fight Jafar for the realm and a final confrontation between Alice and Jafar takes place at the Well of Wonders.