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.
In Agrabah, many years ago, young Jafar asks his dying mother what he should do when she passes. She tells him his real father is the Sultan, who will protect him. She gives her son a ring the Sultan will recognize, then dies.
In Victorian England, Jafar speaks with Alice’s father, Edwin, trying to butter him up with praise of his daughter and her obviously excellent upbringing, but her father impatiently asks after her welfare. Jafar suggests they go see her and dramatically reveals the White Rabbit stowed in his case. The Rabbit grumbles, but makes a hole in the drawing room wall so Edwin can travel with Jafar.
The title card features a small dragon.
Jafar and Edwin arrive on the yellow and red brick road Alice was traveling when she began her quest. Jafar dismisses the Rabbit and calms Edwin, who is wondering if he’s hallucinating or in a dream. Jafar assures him Wonderland is real and very dangerous, especially to a young girl like Alice. Jafar is still maintaining the lie that he’s a doctor from the asylum, lamenting that Alice obviously won't come home on her own, but he suggests she will be delighted to be rescued by her father instead, Edwin corrects him as he nervously cleans his glasses, explaining that he never believed in any of Alice’s stories, so he doesn't expect her to want to hear from him now. Suddenly menacing, Jafar expresses disappointment at this unexpected development.
Alice and the Knave approach the foot of the mountain, debating strategies for getting into Jafar’s fortress at the peak. As they step through the trees, they realize there is no mountain. The fortress is on a floating island, a thousand feet in the air above the sea.
Tweedledee delivers a report to the Red Queen, back in her throne room. The shores have been searched, but no sign of the Genie has been found. He asks, "Have you considered the possibility that he didn't survive the fall?" Disgusted, the Queen replies, "Have you considered the possibility that you are a lazy imbecile?" She exposits her strategy to find the Genie before Jafar returns, but the sorcerer appears behind her just in time to hear her treacherous intentions. He plays it cool until he finally learns Cyrus has escaped, then tries to order the Queen's men to find the Genie. She stops him, saying, “My men answer only to me,” and they posture a bit while recapping their dastardly plans.
In Jafar's dungeon, the Sultan declines to tell Jafar how Cyrus got away. He warns Jafar that he is losing, and when Jafar scoffs that at least he's not stuck in a cage, the Sultan asks, “Are you certain of that?”
Jafar has Edwin cuffed to a chair and drugged. He draws some of the man's blood with a syringe and adds it to a mortar with a few other potions ingredients, which he stirs with the pestle. Edwin says, "You're insane."
Meanwhile, Alice and Knave take an inventory of the contents of their pockets, looking for a way to get to the floating island. Alice has two wishes. She says, “We have to get creative and think!" She finds a birdbark tree, and demonstrates for Will that the branches float when broken off.
While mixing his potion, Jafar casually asks Edwin if he's right-handed or left. When he gets no reply, Jafar provokes Edwin to punch him with his left, and gets his answer that way. He calls his guards to throw Edwin in a cage and stalks away.
In Agrabah, young Jafar has been caught trying to steal a sword from a palace guard, so he is escorted to a private audience with the Sultan. The punishment by law is to lose the hand with which he stole. The Sultan handles these petty thieving matters personally, which is lucky because it gives Jafar a chance to show the Sultan his ring. The Sultan realizes who Jafar must be and agrees to take the boy in as a servant. Jafar says, “I don’t need to be a prince, just a son.” The Sultan responds, "You will be neither." He clearly lays out the expectation that Jafar never acknowledges their true relationship.
Alice tries to convince Knave to jump in a basket they're going to make out of twigs and birdbark so they can float up to Jafar's keep. Knave feels this plan is dangerous, protesting that he has no fear of flying but, "I have a fear of not flying. Of being in your basket, a mile up in the air, and suddenly no longer flying." In the woods nearby, Jafar drinks his potion and is instantly transformed into Edwin.
Jafar, who is now disguised as Edwin runs out of the woods and exclaims that Alice was right about everything. He asks if she can ever forgive him for doubting her, and wraps her in his arms. Alice is too dismayed to speak.
Alice listens while Jafar-as-Edwin gives an overly detailed account of how he arrived in Wonderland. He makes a point to take his glasses out and clean them just as he saw Edwin do earlier. We know she believes he's her father because she finally expresses her bitterness at the way he treated her.
Young Jafar serves ambassadors in the Sultan's court who are asking the Sultan for support for a supply blockade they are having with their northern neighbors. The Sultan insists he cannot help them, and then, he prompts his young son, Mirza, to explain why not. Mirza calmly answers by stating it's against policy. "What policy?", asks a diplomat. Mirza can't remember, but Jafar blurts out, "Foreign policy!" before delving into an explanation for the reasons behind the enforced policy. The Sultan, perturbed that Mirza has been upstaged, manages to smooth this over by jokingly explaining to the ambassadors that even in Agrabah, servant boys are well-educated although they should know better than to speak out of turn. Embarrassed, Jafar apologizes, "My apologies, fath- my apologies."
Young Jafar sits quietly in his little room in the Sultan's palace. Prince Mirza enters and asks his name. After Jafar answers, Mirza tells him, “The correct answer is, ‘I am too lowly for my name to abuse the ears of the prince.’” Then he slaps Jafar hard across the face. The Sultan enters and Mirza starts to apologize, but their father instructs him to hit Jafar again. He says again that Mirza is his only legitimate heir and tells them both, “True power comes from fear.”
In the present, Knave and Jafar, disguised as Edwin sit together, making the basket for Cyrus's rescue. Alice is elsewhere, not wishing for her father's company. Jafar-as-Edwin asks Knave if he was a terrible dad. Knave tells him to focus on what's important to Alice now – getting to the floating island to rescue Cyrus. Jafar-as-Edwin is delighted to hear Alice still thinks Cyrus is up there. He asks Knave for advice on how to get close to Alice again. Knave tells him that Alice will always try to help people in need, then suggests Edwin help find Cyrus, as nothing would go farther to heal their relationship.
Somewhere else, Cyrus is lying unconscious on a beach.
While building the basket, Alice asks Knave if she should forgive her father. He says, "Definitely not," but believes she will, because it's the right thing to do. Nearby, Jafar-as Edwin discreetly casts a spell to sic a fire-breathing dragon on himself. Alice and Knave have a humorous conversation about physics, concerning the descent of the basket once Cyrus is rescued. They spot the dragon flying toward them.
Alice and the Knave successfully use her loosely-woven basket to shield themselves from the dragon flying at them. As they run away, Jafar-as-Edwin joins them but falls flat on his face. He lies uselessly on the ground, calling for Alice to save him as the dragon closes in. Alice throws her sword at it and it dies instantly. She forgives her father and reassures him that she definitely hasn't picked up on his ruse. Jafar-as-Edwin smirks just a little.
In old Agrabah, the Sultan visits young Jafar in his room and accepts his apologies for the earlier incident, then drowns him in his washbasin. He pulls the boy's limp body out of the water and places it on the carpet, ordering the guards in to dispose of the body.
In a hanging cage in Jafar's dungeon, Edwin says grace over his gruel, but grimaces at the first taste of it. The Sultan strikes up a conversation, and Edwin speaks of his great sin, of not believing in his daughter when she asked him to. The Sultan says, “If that is your greatest sin, then you have sinned very little.” Edwin asks if this old guy in the swinging cage knows a way out and just chose not to take it, but the man who is obviously the Sultan says only one man ever escaped, "And I expect to see Cyrus returned in chains at any minute." Edwin is excited to hear that Cyrus, "Alice's Cyrus?" is still alive.
Alice, Knave, and Jafar-as-Edwin cook up some of the dragon meat for dinner, but Alice notices Jafar-as-Edwin doesn't say grace over the meal. Alice immediately acts suspicious and makes up an excuse to pull Knave away. She glances untrustingly over her shoulder at Jafar-as-Edwin, who sees she's onto him. Alice and Knave ditch the imposter, and Jafar summons his staff, returning to his usual appearance.
In Agrabah, young Jafar wakes up in a garbage dump. A mysterious magical energy seems to be floating over him.
Grown-up Jafar storms into his dungeon and grabs Edwin, telling him he is going to die.
Alice apologizes to Will for making him spend the whole day with the imposter. Jafar flies in on his carpet and threatens to drop Edwin, but Alice thinks this is still the imposter. Edwin doesn't blame her for not knowing the difference between him and a big fake. He confesses to blaming her for her mother's death, and for all his unhappiness. He doesn't ask for her forgiveness but grabs the moment to tell her Cyrus has escaped. Jafar has to drop him to stop him from telling her more, but Alice believes this is her real father now, and quickly wishes him home. Jafar smugly reminds her she only has one wish left and flies away.
Knave tells Alice he's sorry. Alice is pretty happy, though. She knows Cyrus is nearby and she's finally made peace with her father. Will reminds her that all magic has consequences and asks what the fallout might be from her wish.
Edwin suddenly wakes on his sofa at home as his wife comes to check up on him. He assumes everything that just happened to him in Wonderland was just a dream.
Jafar visits the man who is obviously the Sultan, and the prisoner asks to speak face-to-face "like a man."
In flashback, Jafar, now grown and armed with his serpent staff, storms the Sultan's palace single-handedly. He prompts the Sultan to look at his face and recognize him and we see the Sultan has aged into the man from the dungeon. Jafar informs his father that his anger kept him alive. Mirza walks into the throne room and Jafar offers to spare the Sultan if Mirza will fight him. Mirza slowly backs away and tries to leave, but Jafar kills him. The Sultan is devastated. Jafar asks him to call him his son. The Sultan says, "You are a bastard boy." Jafar promises that the Sultan will call him son one day.
In the dungeon, the man who is now acknowledged as the Sultan argues with Jafar. He says he regrets not murdering Jafar better when he had the chance and swears again that he will never call Jafar his son. The Sultan doesn't think love will have the same value when it's brought on by a spell. He enacts his only plan of escape and steps off the ledge to fall to his death. Jafar summons the magic carpet to catch him.
On the beach where he's been lying unconscious, Cyrus wakes up and murmurs Alice's name to himself.