Once Upon a Time
A young girl, Alice, climbs out of a hole near where a table with her toy tea set sits. Relieved to be home at last, Alice runs to her home and pounds on the door when she discovers that it's locked. Her father answers and is shocked to see her. When Alice wonders what's wrong, her father tells her that she's been gone a very long time and they thought she was dead.
Later, Alice's father calls in Dr. Lydgate and tells him what Alice has said about a white rabbit and smoking caterpillars. Lydgate figures that Alice is delusional and says that he can cure her.
In the town of Storybrooke, a man walks down the street at night. He goes to Granny's diner as a storm comes up, and Leroy and Ashley Boyd are closing up. They advise him to take cover before the storm starts, and the man tells them that he'll get right on it. He then uses a key to unlock the diner door and go inside. After pouring himself some coffee, he watches as the room shakes. The floor bursts open and a large white rabbit emerges. The man wonders why he's there and the White Rabbit says that they're late for someone: Alice. The White Rabbit reminds the man that he's the Knave of Hearts and Alice needs him.
At the Bethlem Asylum in turn-of-the-century London, Lydgate and his doctors question a grown-up Alice, asking her if she remembers her stories of a murderous red queen, an invisible cat, and a hookah-smoking caterpillar. Alice finally admits that it is preposterous and Lydgate continues, noting that her father was at his wit's end because she kept searching for proof of her claims. The doctor asks if she still believes that it's true.
Alice steals a bit of mushroom from the caterpillar and runs off. She heads into the maze and the Queen's soldiers chase her. Alice eats some of the mushroom and shrinks down to a few inches high.
Alice drifts off for a moment and then admits that she made it up and she never left England. Lydgate asks if she was telling the truth then or now.
The soldiers overlook Alice, who hides in a discarded brass bottle. A man appears ahead of her and asks why she is in her bottle. Alice threatens to drink from a bottle and grow to giant and the man invites her in and introduces himself as Cyrus.
Lydgate asks Alice where she really was and Alice says that she was with a friend.
Cyrus describes his homeland of Agrabah and confirms that Alice is also a stranger in Wonderland. She says that she has to go home soon because she has proof of Wonderland, and briefly takes the disgruntled White Rabbit out of her bag. Cyrus asks who the proof is for, asking if she has some loved one, and Alice assures him that she doesn't. When she explains that she needs proof for her father, Cyrus points out that if he truly loved her then he'd know she was telling the truth. He then offers to grant Alice three wishes.
Lydgate says that if she wishes to leave, she needs to be forthcoming. Alice snaps at him, insisting that she doesn't want to wish for anything. The doctor realizes that she's talking about the genie, who she freed and traveled from world to world with for a time according to her stories. They fell in love, and Lydgate asks if she's willing to admit that was a lie.
Alice and Cyrus travel to the Boiling Sea and the genie explains that in a hundred years he has been tethered to the bottle. His only wish was to be free... until now. Cyrus starts to kneel but Alice tells him yes and pulls him up to kiss him. The genie has an amulet that glows as they kiss, and he says that their hearts are entwined and they'll know when they're near each other. Men advances on them and Cyrus tells Alice to leave.
Lydgate says that Alice was an ignored little girl who made up a fantasy where she could be everything she wanted to be. Crying, Alice says that she doesn't believe it, but Lydgate says that she calls to Cyrus in her sleep every night.
The Red Queen and her soldiers step out onto the cliff and she sends her men to attack Alice and Cyrus. They are soon overwhelmed and the Red Queen throws Cyrus into the sea with a single magical gesture.
Lydgate says that they have a new procedure that can make her forget whoever she is holding onto and take away her pain. He admits that it hurts a little, but far less the pain she is feeling now. Lydgate hands her a pen and invites her to sign the authorization papers, and Alice does so. The doctor tells her to get some sleep because her life will start anew the next morning.
As Alice sleeps in her cell, she whispers Cyrus' name. In the operating theater, Lydgate prepares his instruments and tells the orderlies to fetch Alice.
When her cell door open, Alice demands time to get dressed… and realizes that it's the Knave. She doesn't believe he's really there, but the Knave insists that they have to go. Alice refuses and the orderlies come in and restrain the Knave. She insists that she doesn't want to remember, but the Knave tells her that the Rabbit saw Cyrus: he's alive. When the orderlies beat the Knave, Alice attacks them and knocks them unconscious. The Knave watches, amused, as they go after Alice and she defeats them with ease. She goes to the basement where the Rabbit is waiting and complains that they're late. As they head out, Lydgate finds them and begs Alice to stay so that he can help her get better. He stares in shock as the White Rabbit steps forward, and they go out into the street.
The orderlies come after them and the trio runs down an alleyway only to find themselves in a dead end. Alice tells the Rabbit to start digging and he runs to a wall and creates a portal. The rabbit leaps through but the Knave warns that he didn't leave Wonderland in good terms. Alice reminds him that she helped him get back his heart, and now he has to help he get hers back. As the orderlies approach, the Knave realizes that he has no hope and leaps into the portal with Alice.
Alice and the Knave land on a pond in the Mallow Marsh. Once they regain their footing, they make their way to the dock where the Rabbit is waiting. Alice asks about Cyrus and the Rabbit explains that he meant that he talked to the Dormouse and his friend saw the genie. Cyrus was at the Mad Hatter's abandoned home. The Knave and Alice start sinking into the marsh and the White Rabbit tells them that the Mad Hatter's home is in the Tulgey Woods. He runs to get help as they sink, and the Knave says that he feels like a s'more. When he describes what a s'more is, Alice grabs one of the hovering dragonflies, which are real dragons, and uses its flames to toast the surface of the Mallow Marsh. Once it's solid enough, they pull themselves to safety.
The Knave is ready to leave, admitting that he thought the Rabbit had actually seen Cyrus and he wouldn't have come otherwise. He warns Alice that a lot of people want him to dead and admits that they have good reason. Alice offers to pay him and removes three ruby wishes from a hidden compartment in her boot. When the Knave wonders why she doesn't us them, Alice admits that wishes have unexpected consequences. He figures that he can make a consequence-proof free wish and agrees to get her to Tulgey Woods in return for one wish.
The Rabbit runs through the forest until the Red Queen and her soldiers find hm. She emerges from her carriage and a soldier drags the Rabbit over. He tells her that he came as soon as he could. The Queen takes him to her castle and confirms that he told Alice that Cyrus is alive. However, she warns him that his debt to her is not yet paid. The Queen tells him to inform her everything that Alice says and does, and the Rabbit reluctantly agrees.
The Knave takes Alice to Tulgey Woods and she grabs a branch as a weapon. As they proceed, the Knave asks why the Queen threw Cyrus into the Boiling Sea. Alice admits that she doesn't know but plans to ask her... violently.
At the Queen's palace, the sorcerer Jafar arrives and asks what Alice is doing now. The Queen points out that they want Alice to find Cyrus, and he warns that they can't accomplish what they want until they have the genie's bottle and Alice has made all of her wishes. She tells him to mind his place and Jafar gestures with his staff, saying that he doesn't need her anymore now that she's brought Alice to wonderland. He chokes her with a gesture, but the Queen says that he doesn't know where Alice is. Realizing he still needs the Queen, Jafar releases her. The Queen warns him that he's in her world, not Agrabah, and that she will get the wishes. When Jafar wonders what she wants in return, the Queen tells him that he'll find out in due time and tells him to leave.
Alice and the Knave spot a wanted poster for the Knave and Alice wonders what he did after she left. The Knave tells her not to ask and Alice climbs a tree to try and spot the Hatter's house. She removes her boots to make the climb and the Knave grabs the boot with the wishes as soon as she's gone. Up in the tree, Alice spots the hatter's house but looks down to discover that the Knave--Will—has left. A giant Cheshire Cat appears among the trees and smiles ominously. Alice tries to leave but the Cat cuts her off. It advances on her and Alice realizes that he looks different. The Cat says that Wonderland has grown stranger and there's little food to go around.
The Cat lunges at her and she falls to the ground below. The Cat drops down and comes after her, and she grabs her branch and tries to fend it off without success. It pins her down and explains that the Red Queen promised that she would be an appetizing meal. As it prepares to eat her, the Knave jumps on its tail, distracting it. When it spins around, the Knave throws a piece of mushroom into its mouth. The cat inadvertently swallows it and shrinks down to the of a normal cat. Once it runs off, Alice accuses him of stealing her wishes. The Knave insists that he was protecting the wishes and Alice points out that wishes can only be granted, not stolen.
Alice and Knave continue to the Hatter's house and when they see it, Alice runs ahead, calling Cyrus' name. However, when they go in and they discover that no one is there. The Rabbit arrives and claims that he went back to rescue them. Alice insists that Cyrus but the Knave points out that he might not ever have been there. She realizes that that Cyrus really is gone and goes outside, heartbroken once more.
While the Knave wonders why the Rabbit made Alice lose Cyrus a second time, Alice calls to them. She's found the amulet in the grass, and the Rabbit realizes that if it survived the Boiling Sea then so did Cyrus. The Knave doesn't believe that the genie could have survived and suggests that the Rabbit take them back. Alice refuses and tells him to leave if he's leaving. When the Knave points out that she has no proof, Alice is confident that Cyrus is alive and asks the Knave if he's coming with her. He reluctantly leaves and the three of them walk off.
In a cage suspended in a deep well, Cyrus mutters Alice's name. He remembers falling onto Jafar's magic carpet before plummeting into the Boiling Sea. Jafar arrives and smiles in triumphant.