In Agrabah past, a young Jafar is told he will be cared for by his real father just before his ailing mother passes away. He is given a ring to prove that he is sultan's son. Jafar wears this same ring in the present day as he meets with Alice's father, Edwin. He produces the White Rabbit, who opens the portal to Wonderland. Edwin lets Jafar know that he never believed in his daughter. That's unfortunate. Jafar was hoping there would be a bond between the two of them. In fact, he was counting on it.
The Red Queen lets Jafar know that Cyrus has escaped. There's already a full-scale genie-hunt on for him. Jafar's other prisoner, the elderly man, lets his captor know that he is losing. Elsewhere, Alice and the Knave see Jafar's castle hovering in the air over the lake. They find a birdbark tree. Their wood is amazing. Alice breaks off a branch and watches as it floats up into the air.
In Agrabah past, a young Jafar is brought before the Sultan, who realizes that he is his son. The ruler makes him a serving boy to his family. He orders Jafar to never address him as his father. In the present, Jafar doesn't have time for Edwin to win back Alice's love. So he's going to have to steal it. He sees Alice and the Knave making plans to use the birdbark to fly up to the castle. Jafar drinks a potion he created which turns him into the spitting image of Edwin. Alice is shocked when her father staggers up to stand before her.
Alice is not ready to forgive her father. Her rant against him has Jafar recalling a time in the past when he shows up the sultan's other son in front of some important people. He almost slips and calls him father. Later, the sultan walks in on his son as he is smacking around Jafar. He encourages the beating to continue. Back in the present, Edwin/Jafar asks the Knave for advice on how to get to Alice. He learns that it's in her nature to help people. The Knave also reveals that nothing means more to her than finding Cyrus.
Edwin/Jafar summons a dragon to attack them. When Alice sees that her father is danger, she takes action. She draws her sword and slays the beast through the heart. Alice gives her father a big hug. She forgives him for his past mistakes. She invites him to come with them to rescue Cyrus. Of course, the real Edwin is locked up in a cage with Jafar's elderly prisoner, who says he knows of only one thing Jafar desires. It happens to be the one thing he will never have.
Alice eventually realizes that the man before her is not her father. Edwin/Jafar realizes they are hip to his game. He summons his serpent staff to rise from the ground as he transforms back to his true self. He returns to his castle to bring the real Edwin before Alice, who still doesn't believe it is her father. Edwin's heartfelt words eventually reach her. He lets her know that Cyrus has escaped. With that, Jafar drops Edwin off his magic carpet. Alice has no choice but to use a wish to save her father's life. She wishes him back home. Edwin is safe, but believes his adventure was all a dream.
In Agrabah past, the sultan attempts to drown a young Jafar. The boy appears to be dead, but a magic swirling sand vortex revives him. Jafar has been tossed out of the castle. Years later, a grown up, powerful Jafar infiltrates his father's castle once more. We now see that the sultan is actually the elderly prisoner.
Jafar kills the ruler's other son before him. He orders the sultan to call him his son. If he does this, he will spare him unending pain. This is the one thing Jafar wants. It's the one thing his father said he will never get. He tries to keep his word by jumping into the abyss. Jafar saves him saying that the real fun is about to begin. Outside the castle, a previously unconscious Cyrus suddenly pops awake.