In Victorian England, the young Alice tells a tale of a strange new land that exists on the other side of a rabbit hole. An invisible cat, a smoking caterpillar and playing cards that talk are just some of the things she's seen during this impossible adventure. Surely this troubled girl must be insane and her doctors aim to cure her with a treatment that will make her forget everything.
A powerful dark magician, Jafar has great plans for the young and wilful Alice, related to her lover's magic bottle and the wishes he can great. Jafar originates from the land of Agrabah and has somehow found his way to Wonderland, wherein he will stop at nothing until he gets what he wants, and will try to dispose of those who stand in his way or who no longer are of any use to him.
In the land of Agrabah, the dangerous and powerful Jafar visits a merchant, having noticed all the good fortune that has come his way recently, such as that he earns very little income but his home is very well acquainted, that he has a garden of fresh vegetables out back and two camels outside where most men in the market place can barely afford either.
The merchant tries to argue that he has merely been very fortunate and Jafar comments that he has everything a man could possibly wish for, suggesting that he has perhaps met someone who can grant them. Pretending that his good fortune merely comes from family investments, the merchant makes his way into a back room, telling Jafar that he wants to turn off his stove, when in actuality he wishes to alert his genie, Cyrus, that the man with the serpent staff is there, referring to Jafar. Cyrus, concerned, tells the man to leave, but instead, the merchant wishes for Cyrus to be gone; to be as far away as possible. Jafar bursts into the backroom, outraged that he was unable to steel Cyrus, and the genie's bottle is meanwhile transported to Wonderland with him in it, resting in the foot of the hedges of the Queen of Hearts.
A young girl by the name of Alice is led to Wonderland by the powerful White Rabbit, and when she finally comes home after her adventures in that wondrous place, her father is surprised to find her back, alive and well, as he thought she'd died, claiming she'd been gone a long time. Alice's stories about Wonderland fail to be bought by the people around her, and a psych professional even claims that she's lying and perhaps unstable.
Alice, determined to prove the truth, returns to Wonderland as a young woman to bring evidence of her stay there, and meets a genie by the name of Cyrus, who grants her three wishes. Alice and Cyrus share many adventures in Wonderland and fall in love, eventually leading to him proposing to her. However, their proposal is cut short when the villainous Red Queen - who is in cahoots with the equally nefarious Jafar - shows up and throws Cyrus into the Boiling Sea. Alice believes he's fallen to his death, but in truth he lands on Jafar's magic carpet, all part of a plan he and the Queen came up with. Jafar then traps Cyrus in a giant cage in his palace, up in the clouds that soar over Wonderland.
After Alice and the Knave of Hearts return to Wonderland, having been brought there by the White Rabbit whom, unbeknownst to them, is working under the direction of the scheming Red Queen, with the pretext of rescuing Cyrus the genie, Jafar, who had an agreement with the Red Queen, shows up on one of her palace's balconies and she informs him that Alice is back and looking for her genie, which she implies is what they wanted. Jafar moves closer and tells her that what they want can't be accomplished without the genie's bottle, and Alice's made all her wishes.
He tells her not to be so pleased with herself, and she scolds him for talking down to the Queen. He tells her power is fleeting, which she takes as a threat, but he makes it clear that he's not just threatening her... he's ready to dispose of her. Jafar starts to choke the Queen through magic, but she is able to murmur that he doesn't know where Alice is. He releases her, and the bitter Queen reminds him that he's in her turf now, and if he wants her assistance, their deal remains.
The Queen promises to get him his wishes, and he asks what she wants in return, to which she responds, "All in due time." She then tells him to get back on his carpet and let her deal with Alice. He tells her he hopes she does, for her sake, and then his carpet appears and he steps on it and flies away. Later, Jafar goes to pay a little visit to Cyrus, whom he's got locked up in a giant cage in his palace in the clouds over Wonderland.
When the villagers of Wonderland reunite at the Red Queen's palace to discuss their woes with her, they are frozen by Jafar's magic, for the dark wizard wishes to discuss his plans with his partner-in-crime. The Queen has agreed to find Cyrus' bottle for him, in exchange for getting her unholy desires fulfilled. She asks Jafar if he can truly change the laws of magic using the bottle's power, to make the impossible possible, and the villain confirms this. Later, Jafar realizes that the Queen knows where the bottle is hidden.
She tries to maintain some leverage by imposing that Jafar proves that he can do what he claims he can do before she tells him where the bottle is, but the wizard isn't having any of this. He freezes the Queen and lets her know they are not partners and he doesn't owe her anything; he's given her his word, and that's more than most ever receive. The Queen, looking intimidated, finally tells him where the bottle is: Mimsy Meadows. Jafar flies there on his magic carpet, hoping to find it, and his presence is witnessed by Alice and Will. It turns out that Alice kept telling everyone it was there so that she could know who she was up against. Unable to find anything, Jafar demands that Cyrus tell him where the bottle is, and the Queen shows up and tells him she has it, finally gaining the leverage she wanted.
Cyrus is woken up to witness as the Red Queen and Jafar have dinner before him. Jafar shows him the message he sent to Alice, where she wrote back that she's coming for him. The two villains decide to send a horrid creature after Alice, hoping to scare her and force her to waste away one wish. As the Queen skims through a book of Wonderland's most terrifying inhabitants and suggests them one by one, Jafar admires the look on the genie's face each time she brings up a name. When the Queen suggests the Bandersnatch, Cyrus looks particularly worried, and Jafar picks up on this.
It's settled then, the two partners decide to send a Bandersnatch after the young girl. On their way, Jafar stops to compliment the Queen, starting to acknowledge that there is more to her than her exquisite exterior. The Bandersnatch attacks Alice and Will at the Grendel's house, but Alice, having learnt about such beasts because of Cyrus, is able to overpower it and have it killed. When the female Bandersnatch dies as well (for they mate for life), the Queen believes Alice must have made her wish already. However, Jafar claims that he would have known about it, and is livid once he realizes they were tricked by Cyrus.
Later, the two villains visit the Grendel and ask him what happened. He says - hoping to be reunited with his deceased wife in the process - that he was saved from the beast by a man and a woman. Jafar asks him who the man was, wanting to know who's helping Alice, and Grendel recounts that Alice called him "Knave" (a name that triggers a reaction from the Queen). He then asks if he can be reunited with his wife, and Jafar confirms this... right before he jams the bottom of his staff into the Grendel's chest and kills him.
Jafar confronts the Red Queen about having brought Will to Wonderland to aid Alice without having informed him. When she tells him that the Knave of Hearts was simply a means to an end and that his purpose is now fulfilled, Jafar tells her to remove him from the playfield. Later, Tweedledee, who, unbeknownst to the Queen, is in cahoots with Jafar, informs the dark wizard that the Queen has indeed captured and locked up the Knave. Jafar meets with her and orders that Will be executed in public, to show everyone the price for assisting Alice in Wonderland.
The execution is set up, and the two villains are told that Alice is in the crowd, but Jafar keeps the Queen's minions from doing anything about that, showing interest in seeing what Alice is willing to do to help a friend. Indeed, Alice is able to rescue Will, and they make a run for it in the maze gardens, but Jafar shows up and intercepts them. He chokes Will through magic to try and get Alice to make a wish, and she does just this... and wishes that, if the Knave dies, so does she. Needing Alice alive in order to waste through all her wishes, Jafar lets go of the Knave and tries to torture her into making another one. However, Alice's love for Cyrus is far too strong, so she doesn't cave. Jafar lets her go, but promises to continue exploiting her weakness: her heart. Before he leaves, he turns Will into a stone statue.
Tweedledee captures the White Rabbit and brings it before Jafar, who claims to be intrigued by the magical creature. The dark wizard offers to help the Rabbit with his debt to the Queen, should he provide him with help instead with a little problem of his own: Alice. After all, the Rabbit has known Alice for long now. Jafar grills the Rabbit, hoping to know more about his enemy and who else in Wonderland she cares about, enough that she might wish for their survival, but the Rabbit stalls him, until the villain cuts off one of his paws with the use of his staff. He then gives the Rabbit one minute to come clean, and he says there's someone else Alice cares about, but they're not in Wonderland. Jafar is intrigued. He then reattaches the foot, and says that the Rabbit's help was actually valuable. He then shows interest in making a trip, but the Rabbit makes a run for it, trying to escape the villain. However, he runs into an escaped Cyrus, and, hoping to protect his friend, gives up his own attempt to escape and keeps the villain entertained by taking him wherever he wants to go.
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