Once upon a time, a little girl named Alice climb her way out of a mysterious hole in the ground. She raced home only to learn that her father thought she was dead. Alice, you see, had been gone for a very long time. No one believed her tales of visiting a land with smoking caterpillars, giant mushrooms and a talking white rabbit. Alice was determined to prove she wasn't a liar. This is how her story began a long time ago. It continues in the present day where it has ties to an enchanted town known as Storybrooke.
A mysterious figure walks the streets of Storybrooke unaffected by the storm that's coming. He fixes himself a cup of tea in a restaurant he does not own. A rumbling force shakes the place but the tremors are not from the storm outside. The disturbance comes from inside the restaurant where a talking White Rabbit (the voice of John Lithgow) bursts up from the floor announcing they are late. Someone needs help from the tea drinker since, after all, he is the Knave of Hearts (Michael Socha). The White Rabbit explains that the person in peril is Alice.
A fully-grown Alice (Sophie Lowe) is locked up in London's Bethlem Asylum. She tries to convince a team of doctors that she no longer believes the wild stories she's told about a mysterious Wonderland she once visited after falling down a rabbit hole. While trying to survive the many dangers of the place, Alice met a handsome genie named Cyrus (Peter Gadiot). She sought shelter inside his bottle. They each spoke of their homes. Alice is ready to return to hers now that she's captured the White Rabbit. He's how she'll prove to her father that she's not insane. Cyrus is most understanding and offers three wishes to Alice. The two of them fall in love.
While gazing out at the beauty of Wonderland's boiling sea, Cyrus kneels down to propose to Alice. Their hearts become entwined. This is shown by the glowing red pendant around Cyrus's neck. This magical moment is cut short when the forces of the Red Queen (Emma Rigby) surround them. A mighty battle takes place, but Alice and Cyrus are outnumbered. The Red Queen wants the genie. Cyrus is not going without a fight. He takes down the soldiers, but the Red Queen uses her power to push him over the cliff. Alice watches helplessly as her true love plummets toward the boiling sea below. The red pendant shines as Cyrus disappears into the mist.
In the present day, a distraught Alice agrees to a procedure that will let her to forget her past. She's shocked when the door to her padded cell is opened by the Knave of Hearts, who claims that Cyrus is alive. This has Alice springing into action to take down the hospital thugs who are trying to capture them. She escapes to a hallway where the White Rabbit awaits. One of Alice's doctors sees the talking hare. His patient was telling the truth. Outside the asylum, the rabbit digs a hole which is actually a mysterious portal. He jumps into it followed by Alice and a reluctant Knave of Hearts. Next stop: Wonderland.
Alice and Cyrus hurtle through the portal and land in a spot called the Mallow Marsh. They need to get to the Mad Hatter's house, as that's where Cyrus may be staying. Unfortunately, they are sinking into the marsh. The Knave's mention of s'mores gives Alice an idea. She uses the fire of a dragonfly to toast an area solid so they can climb to safety. The White Rabbit is long gone having hopped off to find help. It turns out he's actually in cahoots with the Red Queen as part of her plan to get Alice back to Wonderland. The White Rabbit is her spy.
The door to the chambers of the Red Queen bursts open. She has a visitor. It's the menacing Jafar (Naveen Andrews). The Red Queen lets him know that Alice is back. That's what they wanted. Jafar corrects her. What he wants can't be accomplished until they have the genie's bottle and the girl has made all her wishes. Jafar begins to choke the life out of the Red Queen until he realizes that only she knows the location of Alice in Wonderland. Their complex alliance is back in play. The Red Queen vows to get the wishes in exchange for a future consideration. Jafar then flies off on his magic carpet.
Alice offers to pay the Knave a wish in exchange for his help. They make their way to the Tulgey Woods. The Mad Hatter's place is on the other side. Alice climbs a tree to get a better view. The Knave steals her shoes when she does this, as that's where she keeps her wishes. Alice has more problems when the oversized Cheshire Cat appears looking to eat her. A battle takes place. The Cheshire Cat is about to devour Alice when the Knave returns to force him to swallow a mushroom. The cat shrinks to a point where he disappears. It appears the Knave had a change of heart. Besides, you can't steal a wish. It has to be granted.
Alice makes her way to the Hatter's house. There are lots of hats, but no sign of Cyrus. The White Rabbit appears to suggest that perhaps he's just at another house. Alice has doubts until she finds the necklace that was worn by Cyrus. It pulses a slow, red glow. Alice can feel in her heart that he is here somewhere. She's going to find him. The Knave agrees to help. As for Cyrus, he truly is alive. Jafar caught him on his flying carpet before he hit the boiling sea. He's kept him prisoner in his castle ever since. There is hope though. Alice is out there. She's searching for him unsure of what she'll have to face in this strange place known as Wonderland.