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.

With the Genie's bottle in her clutches, the Red Queen sends the Bandersnatch after Alice since Jafar needs her in order to use Cyrus (who is discovered to have contacted her). Alice and the Knave of Hearts head to the house of the Grendel in the Whispering Woods to obtain the Forget-Me-Knot so that they can find out who stole Cyrus's bottle before Jafar could steal it. In the Knave of Hearts's flashback, it is shown that he joined up with Robin Hood's Merry Men back when he was Will Scarlet. It is also revealed that Wonderland's Red Queen was once his love Anastasia.

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

Cyrus and Alice reluctantly work with the Red Queen to find Will but must also be prepared to defend themselves from Jafar. Will has troubles of his own when the caterpillar finds the bottle.

Cyrus and Alice uncover alarming information; the Knave must surrender information to Jafar in order to help the Red Queen.