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.

Alice formulates a plan to rescue Cyrus by retrieving his bottle. Meanwhile, the Red Queen begins to question her role in Jafar's plan while they try to find the bottle as well. Also, the story behind how Cyrus got to Wonderland and how he fell in love with Alice is revealed.

When the Knave's life is in danger, Alice has to make the tough decision on whether to use one of her three precious wishes and what that would mean for her and Cyrus. Her new friendship with Lizard reveals some of the Knave's backstory and Cyrus plots to escape. Meanwhile, Jafar's plan to kill the Knave puts the Red Queen in a difficult position as she grapples with her feelings for him and her desire to get what she wants. In flashback, we explore Jafar's origins and find out what he truly wants from Cyrus.

In a flashback, Will Scarlet and Anastasia jump through the looking glass to enter Wonderland against her mother's wishes, since she disapproves of Will. They both soon realize that life in Wonderland isn't exactly what they had both imagined. After being humiliated while attending a ball at the palace, Ana convinces Will to steal the crown jewels in order to get them out of poverty, but in an instant, Ana is caught red handed by the King who makes her a proposition she can't refuse – to marry him and be his Queen to avoid prosecution. Meanwhile, in current Wonderland, the Red Queen convinces Alice to help her acquire magic dust in exchange for information about Cyrus, who in turn has managed to skillfully escape Jafar's castle leaving the White Rabbit in a compromising situation.

Jafar heads to the asylum to find information on Alice; Alice travels to the black forest; Cyrus tries to avoid the Red Queen.

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.