Jafar and Amara work together to cast the spell letting them each ignore the three laws of magic. Alice, kneeling by the dying Cyrus, watches them. Once the spell is completed, Amara goes to her son and Jafar prepares to kill her with a mirror shard, eliminating her only competition. However, the old prisoner comes in, disrupting Jafar's concentration, and suggests that his son have mercy. Jafar refuses, pointing out that his father had no mercy when he tried to drown him as a boy.
With a glance Jafar forces his father to love him, and the old prisoner hugs him and praises him endlessly. After enjoying the brief moment of triumph, Jafar tells his father that he wants him to know what it feels like to be killed by someone he loves. He then gestures and fills his father's lungs with water, drowning him. Jafar then turns to Amara and the others... and discovers that they've escaped.
In the hallway, Amara and Alice carry Cyrus and Alice warns that they won't be able to get far. Amara summons Jafar's magic carpet and they make a quick escape.
Jafar goes to the dungeons and calls out the Jabberwocky, lurking in the shadows. When she steps forward, he invites her to study him and determine what he fears now. After a moment, the Jabberwocky realizes that Jafar fears nothing. He tells her that is true power, draws the Vorpal Balde, and pins her to the wall. Trapped once more, the Jabberwocky wonders what Jafar will do with newfound power. As he douses the lights, Jafar tells her that he'll do anything he wants.
Amara flies Cyrus to the Rabbits' home and Mrs. Rabbit does what she can. Realizing that it's not enough, Amara uses magic to heal Cyrus. As he recover, Alice and Amara introduces themselves for the first time and Amara thanks Alice for being there for her son. The sorceress then tells Alice that next they must defeat Jafar once and for all.
At the palace, Jafar summons the Knave from his lamp and places him within a containing line. He then tells the surprised Knave that he will still uphold his end of the bargain and bring the Red Queen back to life. However, when the Queen comes in, she goes to Jafar and kisses him. As the shocked Knave looks on, Jafar explains that he has broken the second law of magic and made the Queen love him. He then gestures and using his newfound power, raises dead soldiers from a nearby cemetery.
As Alice, Cyrus, and Amara head back for the power, they discuss what to do next. Amara wants to return the stolen water to the Well of Wonders, breaking the genie curse and stripping Jafar of his power. She's well aware that she will lose her own power as well but is willing to accept the cost. Alice points out that Jafar will still have an army and his original powers and says that they need to defeat him. She proposes that she and the Rabbit go to summon the rebel forces and take them to the palace, while Cyrus and Amara take the water to the Well. When the sun comes up, that will be the signal for them to return the water while Alice and her men attack Jafar. Before he goes, Cyrus gives Alice a kiss and his ring, and promises that he'll return to her.
Jafar goes out to welcome his army of resurrected soldiers and tells them that they fight for the good of Wonderland. He orders them to find Amara and her allies, bring them to him, and destroy anything that gets in their way.
Once they gather the rebels, Alice and the Rabbit take them through the forest to the palace. It becomes clear they are uneasy about their chances in the coming battle. Alice sends the Rabbit ahead to scout and addresses the soldiers. She admits that the battle before them is dangerous, and says that anyone who is afraid should leave. However, Alice assures them that they are fighting for the safety of Wonderland and they stand with her, cheering.
As Cyrus and Amara continue to the Well, Amara admits that she's impressed with Alice and how she speaks her mind to her future mother-in-law. They reach the two red doors leading to the Well and the White Knight who guards them.
As Alice and the rebels approach the palace, Jafar's soldiers attack.
More of Jafar's soldiers attack Cyrus and Amara, surrounding them. Amara uses her magic to make them drop their swords, and then forces them to all draw their daggers and kill themselves simultaneously. Cyrus realizes that Jafar will send more soldiers after Alice and tells his mother that they have to hurry.
Despite a valiant attempt, Alice's men are soon defeated and Alice captured. As the Rabbit watches from hiding, the soldiers drag Alice to the palace and bring her before Jafar and the Queen. The Knave explains what Jafar has done to his beloved, and Jafar orders the captive Alice to tell him where Amara has gone. When she refuses, Jafar threatens to break the last law of magic and alter the past so that she never meets Cyrus and dies alone in England. He takes Cyrus' ring from her finger and gives her one last chance to speak.
The Knave, looking on, advises Alice to save herself, but Alice dares Jafar to make good on his threat. However, she assures him that she and Cyrus share true love that is more powerful than any magic. When Jafar points out that he has made the Queen love him, Alice dismisses it as an allusion and pities him because he can never know real love and he can't destroy it.
As Jafar prepares to do as he threatened, the sentry brings a soldier in. The soldier admits that Cyrus and Amara got past them and passed through the doors. Jafar kills the man for his failure and then orders Alice to explain where mother and son have gone. When she refuses, Jafar asks the love-smitten Queen to explain and she tells him all about it, ignoring the Knaves' pleas to stop. Once he knows of the Well of Wonders, Jafar goes to stop them.
Cyrus and Amara approach the Well and Nyx emerges from the waters.
The Queen relaxes on a couch and casually tells the prisoners that they're doomed. The Rabbit sneaks into the room and the Knave, seeing him, tries to distract the Queen while the Rabbit unties Alice. However, the Queen spots him anyway and prepares to kill him. However, the Knave speaks up, trying to convince her that her love for Jafar isn't real. When she insists that their love is perfect, the Knave tells her that love is never perfect, that it's happy and sad, high and low. When the Queen wonders what love is if it isn't what she feels for Jafar, the Knave's true love lets him reach one hand through the barrier line and pull the Queen to him. They kiss and their love shatters the love spell and the barrier line. Coming back to her senses, the Queen tells them that they have to hurry and unties Alice.
Amara starts to offer the water back to Nyx, but Cyrus stops her. He's realized that his mother plans to sacrifice the healing waters and her life, and refuses to let her do it. Amara insists on doing it to break the curse and free her three sons, and after a moment Cyrus releases her. However, Jafar arrives and magically pulls her back and then blasts Cyrus when he draws his sword. He then finishes the job and kills Amara, whose body transforms into water.
Puzzled, Jafar wonders Cyrus hoped to accomplish. The former genie remains silent and Jafar prepares to kill him… just as Alice and the Rabbit arrive through one of the Rabbit's portals. Despite her surprise arrival, Jafar easily immobilizes her and kicks the Rabbit far away. When he wonders how Alice planned to defeat him, she says that she won't be the one to defeat him and yells to Cyrus to return the water. Before he can do so, Jafar magically snatches the water from Cyrus' hand and draws it to his own. He realizes that returning the water would break the curse and free the genies, ending his power.
Jafar tosses the water away and asks Alice what she will do now. Alice reminds him of what she said, that she wouldn't be the one to defeat him. She points out that Jafar took the water, and he realizes too late that he's been tricked. Nyx emerges from the Well once more and tells him that the water wasn't his to take. The Guardian of the Well curses Jafar just as she cursed the brothers, transforming him into a genie. The bracers appears on his wrists and he's sucked into a bottle, and then teleported far away to serve the desires of others.
A wave of energy spreads out from the Well. At the palace, Taj, Rafi, and the Knave are freed from the curse. As they realize that all of Jafar's magic has been undone, the Knave sees the Queen's body and runs to it.
At the well, Alice and Cyrus kiss. They then return to the palace and Cyrus greets his brothers. He breaks the news to them that their mother is dead, sacrificing herself for them.
Alice finds the Knave mourning the Queen's body. He tells her that she did the right thing at the end, but Alice tells him that it isn't the Queen's time. Cyrus comes in with a flask of water and they tell him that Nyx said that it wasn't the Queen's time to move on so she gave her water freely to bring her back. The Knave takes the flasks and gives his love some of the water, and she comes back to life.
Alice and Cyrus are looking out over Wonderland and Alice says that she's ready for a new adventure. Cyrus agrees and when the Rabbit comes out to ask where they're going next, Alice tells him that she's going home.
Later, Alice is in her bedroom putting on her wedding dress. Her father Edwin comes in and says that she looks beautiful, and thanks her for proving that Wonderland exists and that his brief time there wasn't a dream. He's glad to have Alice back and welcome Cyrus into their family, and begs her forgiveness for doubting her in the past.
Edwin then takes his daughter to the main room where Alice's friends from wonderland have gathered to celebrate her wedding to Cyrus. The Rabbit acts as the minister and declares them husband and wife, and then tells the couple to kiss.
Afterward, everyone prepares to leave and the Knave admits that he and the Queen have a lot of cleaning up to do. They hug and Alice thanks the Rabbit for taking her to Wonderland for the first place. He assure her that Wonderland where the special ones find themselves. The Knave starts to go but Alice runs to him and they hug, and she tells him to make sure never to lose his heart again.
Several years later, and Alice is reading the story of her adventures in Wonderland to her daughter. Her daughter suggests that she might publish it as a book, and Alice agrees. Cyrus comes out with tea and the family celebrates together... while the Rabbit watches them from the bushes.