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.
Emma, Mary Margaret, David, Regina, Mr. Gold and Hook enter Neverland to search for a kidnapped Henry, they're greeted by a school of not-to-friendly mermaids who threaten to end their search before it begins; Henry finds himself on the run from the Lost Boys with another escapee from Peter Pan's encampment; and Neal, recovering from his wounds, travels through the Enchanted Forest with Mulan in an attempt to learn the fates of Emma and Henry.
While Emma, Mary Margaret, David, Regina and Hook continue their search for Henry in Neverland, Peter Pan appears before a startled Emma and offers her a map that will reveal her son’s whereabouts. But the only way to make the map appear is for Emma to stop denying who she really is and come to grips with her true feelings about her identity – and Mr. Gold receives some unexpected advice from a friend that could lead him to understand his life’s journey while in Neverland. Meanwhile, in the Fairy Tale Land that was, when the Evil Queen presents Snow White with an offer to live her life with Charming in peace – with the caveat that she give up her claim to the throne – Charming makes it his mission to ensure that Snow doesn’t take the offer.
In their continuing quest to find Peter Pan's hideout and save Henry, Hook suggests tracking down Tinker Bell in the hope that she will lead them straight to his camp. Pan reveals to Henry why he has brought him to Neverland and in the Enchanted Forest, Neal has a plan that could transport him to Emma, but it would involve using one of Robin Hood's most precious possessions. Meanwhile, in the Fairy Tale Land that was, Tinker Bell offers to help Regina improve her life.
Mr. Gold makes a decision to confront Pan, but will he go there to save Henry or give in to the prophecy that the boy will be his undoing? Neal finds himself back in Neverland and in the custody of one of Pan’s most loyal Lost Boys. And David struggles for his life as the poison continues to take its toll on him. Meanwhile, in the Fairy Tale Land that was, Rumplestiltskin goes in search of a missing Bae, who has followed a mysterious figure who steals away children with his music.
With the deadly Dreamshade coursing through David’s body and close to death, Hook takes him on one last journey to find a sextant that could help them decipher a map that would lead them off Neverland. Meanwhile, in the Fairy Tale Land that was, Killian Jones – aka Hook – and his brother, Captain Liam, sail off under orders of the King to find a powerful indigenous plant on an uncharted land that could help heal any injury.
Back in the Fairy Tale Land that was, when Ariel saves Snow White from drowning in the ocean's depths, Snow returns the favor by helping her new friend get acquainted with Prince Eric, with whom she has fallen madly in love with. Meanwhile, Emma, Mary Margaret, David and Hook attempt to save Neal, who is imprisoned in one of Pan's encampments, and Regina and Mr. Gold begrudgingly team up to find a way to take down Pan.
Mr. Gold and Regina send Ariel back to Storybrooke with an item that will allow Belle to locate a hidden artifact that could help take down Pan. But unbeknownst to them, two men have broken into the town with the intent to stop them - at all costs. Meanwhile, Emma, Neal and Hook attempt to find Dark Hollow, where Peter Pan's shadow dwells, in order to capture it, and Mary Margaret is upset with David for keeping his poisoning a secret from her.
Pan leads Henry to a secret cave, where he has convinced the boy that he alone can save magic – and Neverland itself. But a showdown between good and evil is about to go down as Emma, Mary Margaret, David, Regina, Mr. Gold, and Hook find themselves directly on a path to Pan in an effort to save Henry.
The race to stop Pan is on as Henry's life hangs in the balance; with Mr. Gold's help, Regina decides to adopt a baby.
Pan's plan threatens the citizens of Storybrooke's joy over Henry's return; Snow and Charming spend their honeymoon searching for a mythical being that could stop Regina.
The residents of Storybrooke race to stop Pan from placing another curse on the town.
In New York, Hook tries to get Emma to remember who she really is. In the past, the Storybrooke residents return to the Enchanted Forest and are threatened by a threat like no other.
In New York, Hook tries to make Emma remember by something very powerful: true love. In the Enchanted Forest, Regina, Snow, and Charming all team up to defeat a very powerful witch. In another world's past, a young girl learns how to use wizardry only to be hunted by a mob.
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.
Hook and Emma try to find their way back to the present and correct the mistakes they made in the past.