Alice returns home to her father telling her that everyone thought she was dead. Her imaginative stories about a talking White Rabbit and a mystical place called Wonderland end up getting her admitted into an asylum where Dr. Lydgate convinces her to have a procedure that will allow her to forget her pain. Right before the operation is set to take place she is rescued by the Knave of Hearts who takes her to the rabbit who informs her that her true love Cyrus is still alive. As the trio then jumps into the portal returning to Wonderland, Alice sets out on a quest to find him but the villainous Jafar and the Red Queen have other plans for her.

In Wonderland, Alice concocts a plan to find Cyrus and uses his genie bottle as bait to find out who she's up against and who her real friends are. Meanwhile, the Red Queen and Jafar face off and in flashback, viewers find out how Alice and Cyrus fell in love and how Cyrus ends up in Wonderland.

In a flashback, viewers are introduced to Will Scarlet, who turns out to be the nifty Knave of Hearts. Will has joined Robin Hood's Merry Men and convinces them to steal gold from Maleficent's castle before also pilfering an enchanted looking glass for himself that comes with a hefty consequence. Meanwhile in Wonderland, Cyrus successfully tricks Jafar and the Red Queen into sending a Bandersnatch after Alice who in turn exposes something the White Rabbit has been secretly hiding.

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 tohug 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 travels to Victorian England to find a weakness that he can use against Alice. Meanwhile, the newly-restored Knave seeks out Alice, who has fallen afoul of a beguiling trap. And in the past, Alice returns home after losing Cyrus and is reunited with her father Edwin... and meets his new wife and daughter.

Jafar brings Edwin to Wonderland in a ploy to trick Alice into using another of her wishes. Meanwhile, Alice tries to enter Jafar's palace, and in the past, Young Jafar's mother dies and sends him to his real father: the Sultan. However, the Sultan is less than happy to see him.

In flashback, we learn about Cyrus' origin story while Alice seeks out the White Rabbit for answers involving his actions in Wonderland. Meanwhile, the Red Queen and Jafar's disdain for one another comes to a head, followed by a series of chaotic events. The insurmountable consequence caused by their showdown will put everyone in danger and lead to a drastic change.

The Knave is released from the bottle by Lizard and she is given the opportunity to make her dreams come true with three wishes. Cyrus, and a reluctant Alice, partner with the Red Queen to find and rescue the Knave, while the Red Queen is captured by peasants who want payback for her cruel reign. Meanwhile, Jafar has taken over the Red Queen's castle and learns of a fearful creature called the Jabberwocky who he plans to ally himself with.

In flashback, Cyrus' actions lead to a fateful day that leaves his mother near passing, resulting in a decision that comes with a binding price he and his brothers have to pay. Meanwhile, after banding together, Alice, Cyrus, The Knave and the Red Queen split up into two groups that leaves the Knave and the Red Queen face to face with the fearful Jabberwocky, and Cyrus' guilt about his past tests his relationship with Alice.

Alice and Cyrus discover alarming information involving prisoners Jafar has under his control and changes their priorities. Meanwhile, the Red Queen is in critical danger and no one can help her except the Knave by surrendering information to Jafar that he's been desperately seeking. In flashback, Anastasia is about to marry the King and strikes up a friendship with Cora that directly impacts Will. Cora also confronts Will resulting with him asking her for a shocking demand.

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.