The third season revolves around the main characters travelling from Storybrooke to Neverland to retrieve Henry Mills, featuring crossover episodes connecting with the spin-off Once Upon a Time in Wonderland.
Unfriendly mermaids threaten those searching for Henry in Neverland; Henry and another escapee from Peter Pan's encampment go on the run; a still-recovering Neal travels the enchanted forest with Mulan in search of Emma's and Henry's fates.
Peter Pan offers Emma a map that will help her find Henry, but she must come to terms with who she is in order to use it; Mr. Gold gets unexpected advice; Charming works to stop Snow from accepting a deal from the Evil Queen.
Hook suggests finding Tinker Bell and following her to Peter Pan's hideout; Pan tells Henry why he brought him to Neverland; Neal comes up with a plan that could transport him to Emma; Tinker Bell offers to help Regina.
Mr. Gold decides to confront Pan; one of Pan's most loyal Lost Boys holds Neal captive; David fights against the poison; Rumpelstiltskin searches for Bae.
Hook brings ailing David with him to find the sextant that may help them decipher a map that shows the way out of Neverland; Killian Jones and his brother sail off to find a plant in an uncharted land.
To repay Ariel for saving her life, Snow White helps her get acquainted with Prince Eric; Mr. Gold and Regina begrudgingly agree to work together to take down Pan.
Ariel is sent back to Storybrooke with an item that will help Belle find a hidden artifact; Hook, Neal and Emma set out to capture Peter Pan's shadow; Mary Margaret is upset that David concealed his poisoning.
Pan tries to convince Henry that he can save magic and Neverland; a young Rumplestiltskin receives a magical item that could give him a fresh start with his father.
While Henry's life hangs in the balance, the race is on to stop Pan from gaining full magical powers from the heart of the truest believer. Meanwhile, in Storybrooke of the past, Regina decides to fill a void in her life and, with Mr. Gold's help, sets out to adopt a baby.
The residents of Storybrooke are overjoyed upon the return of Henry and our heroes from Neverland. But unbeknownst to them, a plan is secretly being put into place by a well-hidden Pan that will shake up the very lives of the townspeople. Meanwhile, in the Fairy Tale Land that was, Snow White and Prince Charming’s honeymoon turns out to be anything but romantic when they go in search of a mythical being that could stop Regina cold in her tracks.
The race is on to stop Pan from enacting another curse on the residents of Storybrooke, which could kill every living soul in town.
After Rumplestiltskin sacrificed his life to stop Pan from enacting another curse, Regina obliterated her original curse, which erased Storybrooke from existence and whisked its residents back to Fairy Tale Land – leaving Emma and Henry back in our world with no memories of Storybrooke. But all is not well back in the Enchanted Forest when Hook comes calling on Emma in New York City in an attempt to jog her memory so that she can once again help her fairy tale family and friends out of a desperate situation.
Emma arrives in Storybrooke with Henry and reunites with her friends and family, only to discover that no one remembers how they were transported back – or the past year they had spent back in Fairy Tale Land. But Emma is sure that someone in town is responsible for this new curse and teams up with Regina in an attempt to uncover their identity. Meanwhile, in the Fairy Tale Land that was during the past year, Regina, with the aid of Robin Hood, attempts to break into her castle.
While Emma, David, Regina and Hook continue their search for the Wicked Witch, she, in turn, is planning a dark surprise for David, and Zelena’s prisoner is powerless under her watch as she plots her next course of action against the townspeople. Meanwhile, in the Fairy Tale Land that was in the previous year, Prince Charming stumbles upon Rapunzel, who is trapped inside a tower, and must help her confront her fears in order for her to be free.
Neal finds himself back in Storybrooke and yearns for a way to reconnect with his son Henry, whose memories of his father are gone, while also trying to find his own father, Rumplestiltskin, whom he has just learned is alive but missing, and Regina discovers a possible connection with Robin Hood. Meanwhile, in the Fairy Tale Land that was over the past year, agonizing over the death of his father, Neal - with the help of Belle and enchanted candelabra Lumiere - attempts to find a magical solution to bring back Rumplestiltskin from the dead.
With Rumplestiltskin as her slave, Zelena challenges Regina to a fight to the death and shocks the Evil queen with the reveal of their familial connection, and the town lays Neal to rest. Meanwhile, back in the past in the land of Oz, a jealous Zelena asks the Wizard to send her to Fairy Tale Land after discovering that she has a sister, Regina, and that Rumplestiltskin is training her to become a powerful force to be reckoned with.
Ariel returns to Storybrooke and pleads with Hook to help her find Prince Eric, who never returned to the town when the new curse was invoked. Emma agrees to let Regina teach her how to use magic so that she can help defeat Zelena, and Mary Margaret and David try to prove that they can be just as much fun as Hook is with Henry -- who thinks they are boring. Meanwhile, in Fairy Tale Land during the past year, an angry Ariel confronts Hook over her missing Prince Eric, who she assumes was kidnapped and possibly killed by the swarthy pirate. But when Hook confesses that the Jolly Roger has been stolen and Eric is most likely the thief’s prisoner, Ariel unknowingly provides him with a clue as to who the culprit is, and Hook – with Ariel in tow - goes off in search of his ship.
After Zelena steals Regina's heart, Regina casts a spell so that she can speak across the realms to her dead mother, Cora, to discover the truth about why she abandoned Zelena, and Belle stumbles across what Zelena's ultimate end game is. Meanwhile, in the Fairy Tale Land that was, young Cora is duped by a man claiming to be a prince and finds herself alone and pregnant. But a chance meeting with a real prince could lead Cora to the royal life she's always craved, but she must keep her pregnancy a secret or risk losing everything.
Zelena threatens to kill Henry if Hook - whose lips have been cursed by the Wicked Witch -- doesn't proceed with kissing Emma, which will drain all of her magical powers away, and things begin to heat up between Regina and Robin Hood. Meanwhile, back in the Fairy Tale Land that was during the past year, Snow and Charming go in search of Glinda, The Good Witch of the South, to see if she can help them defeat Zelena, and the curse that will ultimately send the Fairy Tale characters back to Storybrooke is cast -- but from an unlikely source.
With Mary Margaret in labor and due to give birth at any moment, the residents of Storybrooke go on high alert in an attempt to ensure that Zelena doesn't try to steal her newborn baby for use in her ultimate game plan to turn back time and change her destiny -- while obliterating Regina's existence. Meanwhile, in the land of Oz of the past, Glinda tries to convince Zelena to fight her evil tendencies and join her and her sister witches as a protector of Oz. But the appearance of a young girl from Kansas could turn out to be her undoing.
While Mary Margaret and David celebrate the naming of their son at a coronation in Granny's Diner, Emma and Hook are pulled into Zelena's time portal and find themselves in the Enchanted Forest of the past. But in their quest to discover a way back, they must be careful not to change anything or risk altering the lives of their friends and family - as well as their very own existence.
In the conclusion of two-part episode that serves as the season three finale, Emma and Hook must find a way to return to Storybrooke, but in their quest to return, they have to find a way not to interfere or tamper with the events that lead up to the first curse, or else they risk altering the entire timeline, and could end up warping the future existence of everyone involved, including Emma, Hook, as well as Emma's family back in present-day Storybrooke.