Emma gets the Lost Boys to tell her where Pan is. Henry is saved and all prepare to leave Neverland and go back to Storybrook. Everyone appears to have found their happy ending now that Pan is gone. Or is he?
Emma Swan's world is turned upside down on her 28th birthday when the son she gave up 10 years earlier knocks on her door. Holding a book of fairy tales he claims are real, he tells her that she's not only in the book but that she is the only hope her people have of being freed from an evil curse.
At Henry's urging, Emma convinces Mary Margaret to pay a visit to a comatose John Doe in the hospital and to read to him from the storybook. But Mary Margaret is stunned at the outcome of her visit. Meanwhile, back in the fairytale world, Prince Charming meets Snow White for the first time in a most unexpected way.
As Sheriff Graham deputizes Emma, the ground shakes and a giant sinkhole mysteriously appears at the edge of town. But a curious Henry's life is placed in danger when he decides to explore the innards of the sinkhole to see if its contents can link the inhabitants of Storybrooke to the fairytale world. Meanwhile, back in the fairytale world, Jiminy Cricket yearns to leave the family business and transform into the person he wants to be.
David - aka John Doe - must choose between staying with Kathryn or leaving her to be with Mary Margaret, with whom he's fallen deeply, and inexplicably, in love; and Emma catches Sheriff Graham in a lie. Meanwhile, back in the fairytale world that was, Prince Charming is about to encounter a life-changing event that will forever alter his destiny.
One of the town's residents begins to remember their fairytale past, and Storybrooke mourns the loss of one of their own. Meanwhile, in the fairytale world that was, the Evil Queen attempts to find a heartless assassin to murder Snow White.
Regina and Mr. Gold play dirty politics and take opposite sides when Emma runs for a coveted Storybrooke public office against Sidney. Meanwhile, back in the fairytale world that was, Rumplestiltskin tries to track down the ultimate power source in order to help his son avert the horrors of a meaningless war.
Feeling their pain from having lived through the same experience, Emma desperately tries to help two homeless children find their birth father before they're separated and put into the foster care system. Meanwhile, back in the fairytale world that was, the Evil Queen coerces Hansel and Gretel into stealing an important artifact from a blind witch.
Mary Margaret and David continue to grapple with their unrequited love, and Emma and Regina grow suspicious over a mysterious new stranger in town. Meanwhile, in the fairytale land that was, Snow White yearns to ease her breaking heart as Prince Charming's wedding to King Midas's daughter approaches.
A dejected Sidney enlists the aid of Emma to help uncover evidence that could expose Mayor Regina as the corrupt person she really is to the townspeople of Storybrooke; and Mary Margaret and David continue their secret rendezvous while trying to figure out a way to unleash their unrequited love. Meanwhile, back in the fairytale land that was, King Leopold, who is the father of Snow White and married to the Evil Queen, stumbles upon a magic lamp and is granted three wishes by a Genie - who warns the king to be careful what he wishes for.
After Mr. Gold's house is robbed, Emma keeps a close eye on him when it looks like he wants to track down the criminal and dole out some vigilante justice as payback, and Valentine's Day finds Mary Margaret, Ruby and Ashley having a girls' night out. Meanwhile, in the fairytale land that was, Belle agrees to a fateful deal to give up her freedom in order to save her town from the horrors of the Ogre war.
With their love for each other growing stronger, David finally agrees to tell Kathryn about his relationship with Mary Margaret and put an end to his loveless marriage. Meanwhile, in the fairytale land that was, while runaway groom Prince Charming searches for Snow White, he agrees to aid Abigail on a dangerous mission to recover something precious that was lost to her.
Mary Margaret teams up with Leroy, Storybrooke's resident trouble maker, to help him sell candles during the Miner's Day Festival. Emma investigates Kathryn's sudden disappearance. Meanwhile, in the fairy-tale land that was, the Seven Dwarfs are made known as well as Grumpy's romance with the beautiful, yet clumsy, fairy Nova.
Mary Margaret hires Mr. Gold as her attorney when Emma is forced to arrest her for the suspected murder of David's wife, Kathryn. Meanwhile, back in the fairytale land that was, Prince Charming sets out to stop a determined and unhinged Snow White, whose memory is still clouded by Rumplestiltskin's potion, from assassinating the Evil Queen.
Emma leaves in search of Mary Margaret and instead finds herself trapped in the house of a seemingly dangerous man named Jefferson. In fairy-tale land, the Queen calls upon the Mad Hatter to help her find something she has lost in exchange for his daughter's safety.
The Evil Queen convinces Snow White to eat her apple. Meanwhile in Storybrooke, she finds a way to retrieve the fruit to get rid of Emma who is ready to make a deal with Regina to leave town while maintaining visitation rights with Henry.