In London, a man is painting in a field when Jafar smashes up out of the ground with the help of the White Rabbit. Jafar asks where he can find Bethlem Royal Hospital, and the man stutters in shock. He finally gives Jafar directions, and Jafar compliments him on his suit.
Later, Jafar arrives at Bethlem, wearing the painter's suit. He goes to see Dr. Lydgate, who is taking laudanum, and claims to be Dr. Sheffield. Jafar asks about Alice and Lydgate claims that he doesn't recall the girl. The sorcerer knows better and points out that Alice escaped with the help of a talking rabbit that Lydgate himself saw. Jafar then takes the White Rabbit out of his bag and Lydgate begs him to put it away. He says that he tried to forget it, and Jafar shuts the bag and then tells him to reveal everything he knows about Alice.
The Red Queen goes to Jafar's dungeon with one of the Tweedles and discovers that both Cyrus and the guards are gone. She turns to the old prisoner and asks what happened, but he refuses to talk. The Queen slams him around and the prisoner tells her that Jafar took Cyrus away. She points out that Cyrus' cage is cut open and demands the truth, and the old prisoner says that the Queen will never catch Cyrus because he carries the greatest power of all: true love.
Cyrus climbs down the side of the mountain as the guards sound the alarm. Once he reaches the ground, Cyrus concentrates and calls to Alice, asking where she is. He sees Alice's necklace glowing in the distance.
Alice looks to the west and realizes that Cyrus lies in that direction. She continues off through the woods and two thieves block her path. They warn that she'll end up in the Black Forest if she continues west, but Alice says that she'll continue regardless. The thieves demand the necklace as toll and Alice draws her sword and attacks them. Once she defeats them, she takes a brand from the fire to light her way and vows not to lose the necklace again.
One Year Ago – Victorian England
Alice emerges from the rabbit hole and discovers that Cyrus didn't follow her through. She breaks into tears. A young girl, Millie, runs up and asks if she's okay. Millie asks if she's okay and Alice says that she used to live nearby. Millie's parents call for her and Millie calls them over. Alice is shocked to discover that Millie's father is her own father, Edwin. She runs to hug him and says that Cyrus is gone and she killed him. When Edwin asks what she's talking about, Alice says that the Red Queen killed him. He tells Alice that she's home now and introduces her to Millie as her half-sister. Alice realizes that Edwin has remarried, and he introduces her to Millie and her new mother, Sarah.
Alice approaches the Black Forest, ignoring the warning signs, and finds a shadowy barrier blocking the path. Bracing herself, she steps through.
The Knave walks through the woods, clutching at his head, when he comes across a peddler. He explains that he was recently turned to stone, and the peddler gives him a waterskin before going along. The two thieves approach the Knave and claim that Alice attacked them in their sleep. They want him to warn Alice that they'll kill her if they meet her again, and tell him that Alice is heading for the Black Forest.
Alice makes her way through the shadows, walking west in a straight line as best she can. As she stares in horror, the torch goes out. However, a light shines ahead and she realizes that she's made it through. She runs and finds herself in a forest with trees emitting purple fumes. Alice breathes in the fumes and the Carpenter comes up and says that the fumes make people feel most mimsy. He explains that they're in the Boro Grove, the most beautiful place in the world, and suggests that she put down her sword and stay for a while. Alice says that she has something important to do but is unable to remember what it was. Smiling, the Carpenter tells her that she must stay and Alice agrees.
Alice listens from the next room as Edwin and Sarah discuss what to do with her. She quickly sits down as Edwin comes in and assures her that he can get her new things. First he would like to know his how long she's staying. Alice says that she is staying forever because there's nothing for her in Wonderland, and Edwin tells her that he has a new family. If Alice wants to stay, she can't mention anything to Millie about Wonderland and Cyrus. Alice points out that he gave up Alice and her mother, and Edwin says that he finally realized that he had to stop clinging to unhappy memories. She says that she can't do that, and Edwin says that she must try to fit in if she wants to stay there. Alice says that she has nowhere else to go and promises to try, and asks if he really wants her there. Edwin takes her hand and assures her that he does.
The Red Queen and Tweedle follow Cyrus' trail. When he says that she can't follow him dressed as she is, the Queen slaps him and says that she wasn't always queen, and that she knows how to get her hands dirty. If she can find Cyrus then she'll have the genie and his bottle, letting her win the game over Jafar.
The Knave makes his way through the Black Forest to Boro Grove and gets a face full of fumes. Alice runs over and hugs him, and says that everything is wonderful there. She shows him a sculpture she made out of flowers, while the Carpenter comes over and stares at them. The Knave asks how long she's been there and Alice doesn't remember. He notices that she has left her necklace on her sculpture and asks why she's abandoned Cyrus, and Alice says that she did it because it made her happy.
Alice joins her new family at the dinner table, wearing a new dress. Sarah says that they must discuss Alice's social obligations and says that she must meet a suitable young man and move on with her life. She has already arranged a tea with a neighbor woman with an eligible son, and Edwin assures her that it will help her forget her troubles. Alice shatters the glass in her grasp and says that she can't handle meeting with young men now.
Cyrus runs through the forest to avoid Jafar's guards and comes to a stream. He walks in the sand and then backtracks in his own footprints to lead them off the track. The guards assume that he went into the stream and continue on.
Alice continues to prance around Boro Grove and insist that there's nothing wrong with her for the first time in her life. The Knave goes to the Carpenter and asks what he did to Alice, but the man simply smiles and stares into space. When the Knave grabs him, he notices that the trees have started to grow up around the man. Looking around, the Knave realizes that all of the trees contain people that fell under the influence of the fumes. He runs to Alice and says that they have to leave, but she doesn't recognize her own name.
Alice is sleeping and having a nightmare about Cyrus. Millie comes in to comfort her and assures her that bad dreams aren't real. She asks who Cyrus is and Alice explains that he's someone very special that she can't forget no matter how hard she tries. Millie wants to meet someone like that and Alice assures her that when she does, she won't wish for anything else. Sarah and Edwin come in and order Millie to bed. Once she leaves, Edwin tells Alice to have the decency to keep her foolishness to herself. Sarah admits that they were wrong to think she could forget and leaves with her husband.
The Knave tries to drag Alice out, but she grabs her sword, refusing to leave. She insists that she's the person she always wanted to be, and the Knave says that it's not real happiness. He explains that since Alice got his heart back, he hasn't used it properly and feels that he still owes her. That's why he can't let Alice stay, and tries to grab the sword. She shoves him away and a tree grows up around her. The Knave admits that the only way she can leave is if she wants to go. He tells her to look at herself, and she stares at the roots growing around her... and says that she's finally found a home.
The Red Queen follows Cyrus' trail to the stream and uses a spell to confirm that he laid a false trail.
Alice is having breakfast when Sarah and Edwin bring in the Darcy boy. Disgusted, Alice says that they don't know her at all and that it won't make her forget. She storms out and Edwin goes after her. He points out that she has nowhere else to go, and Alice says that she won't apologize or marry someone she doesn't love. Alice asks if Sarah makes him happy like her mother did, and Edwin says that they can't spend their whole lives in mourning. He tells her that she has to move on, but Alice says that she can't forget her love in just a few days when it took Edwin years. Edwin snaps at her, saying that his wife was real, and Alice insists that Cyrus is also real. She tells her father that she can't forget Cyrus, and he says that she can't live there. Edwin suggests that she go to Bethlem, but Alice insists that she isn't mad. Her father tells her that she can choose to go the Bethlem or find a husband, but she can't pine for a make-believe life.
The Knave warns Alice that she's running out of time and has to choose. He picks up the necklace and reminds her that Cyrus gave it to him. The vines attack him, dragging him to the ground, but the Knave says that Alice wouldn't be happy until she's reunited with Cyrus. He tosses the necklace to Alice, who catches it and remembers everything. The vines release the Knave as Alice cuts herself free.
Cyrus comes to the edge of a cliff overlooking the ocean far below. The Red Queen comes up behind him as Cyrus realizes that the castle is on an island of rock floating high in the sky.
Alice waits outside the house for a carriage to arrive. Inside, Edwin and Sarah watch and Sarah says that it will be all right. She insists that Alice made the right decision and assures Edwin that Lydgate will take good care of Alice. The carriage arrives and Dr. Lydgate takes her bag. Edwin is disappointed that Alice doesn't want him to visit her at the hospital, and Sarah says that it's time for Alice to grow up. Millie runs up and Alice sees the three of them together as she leaves.
As they leave the Boro Grove, Alice thanks the Knave for helping her. She feels the pain of all her troubles coming back, and the Knave assures her that she'll be fine. He thanks her for transforming him back, and Alice says that it wasn't her. Alice realizes that Anastasia used the magic dust to free him, and the Knave says that he made sure he couldn't love her back a long time ago. When Alice demands an explanation, the Knave tells her that he never put his heart back in. He couldn't bear to feel the heartbreak of his romance with Anastasia, and he eventually grew used to living without a heart. Alice wonders what he did with his heart, but the Knave says that he'll tell her later and points out that her necklace is glowing.
Cyrus vows that he'll see Alice again, but the Red Queen warns that sometimes love isn't enough to conquer reality. The genie sees Alice's necklace glowing in the distance and dives into the ocean below.
Jafar goes to Edwin's house and tells him that he can help him. The sorcerer says that he knows where Alice went after she escaped from the asylum, and he can take Edwin to her.