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.

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.

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.

When Alice discovers that her father is in Wonderland, they begin healing their broken relationship, which leads to her having to make a difficult decision. In flashback, a young Jafar is emotionally distraught after his mother dies and we find out what drove him to become the unforgiving villain he is today.

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.

In flashback, the Knave hunts Alice per Cora’s directive and he finds himself striking a deal to get his heart back, while in present day Wonderland, Alice and the Knave’s friendship is tested as he does Jafar’s bidding and steals from her. Meanwhile, the Jabberwocky attempts to free herself from Jafar’s control and Jafar is confronted by his former partner.

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.