The event of Emma being taken by the Darkness has the Storybrooke residents seeking a way to bring her back, and the only way to make it happen is to turn to an unlikely person: Zelena. However, the wicked witch has other plans in mind, only to be thwarted by Regina, who uses Zelena's magic to activate the Apprentice's wand, which creates a portal that brings everyone to the Enchanted Forest.

They find a bewildered Emma, who is trying to track down Merlin, and along the way befriends Merida, while being guided by a dark apparition of Rumplestiltskin, who wants Emma to embrace the Darkness. After they meet up with King Arthur in their quest in Camelot, the residents return to Storybrooke six weeks later, with no memories of what happened in Camelot, while wearing completely different attires. And Emma is now a fully-fledged Dark One, who vows vengeance on her loved ones.

The Storybrooke residents try to keep Arthur and the rest of Camelot from revealing their identities and prevent Emma from going dark as they search for Merlin, so Regina pretends to be The Savior in order to save Emma. Unfortunately, as the residents are feted at a ball in their honor, Percival catches on to the deception, attempts to avenge himself on Regina. In the ensuing fight, Robin is stabbed with Percival's enchanted sword, but David kills Percival.

Regina begs Emma to save Robin, but despite Hook's plea not to, Emma does so, and results in Regina eventually paying the price. In Storybrooke, the residents, and the now-transplanted Arthurians, are becoming fearful of Emma as the Dark One, and Regina must step up when a demon called the Fury attempts to take Robin's soul as payment, due to Emma having saved him on Regina's behalf. Meanwhile, Hook is feeling that Emma's good side is no longer there, while Henry meets a girl named Violet. It is revealed that Emma brought the Excalibur sword with the stone to Storybrooke, but she can't pull out Excalibur to make it whole unless she pays the price.

In Camelot, the quest to free Merlin continues when Arthur and David head to The Forest of Eternal Night, and fight to obtain a toadstool called the Crimson Crown, which can allow them to communicate with Merlin. In the present, Emma manipulates Hook in order to gain Hook's sword. In the end, Emma brings Mr. Gold out of his coma by using Hook's sword, which had touched him prior to him becoming the Dark One.

She informs the newly awakened Gold that she is going to mold him into a hero who can remove Excalibur from its stone. King Arthur's true intentions are revealed in Camelot and start to emerge in Storybrooke when uses his squire, Grif, to deceive David into believing that Grif had stolen key items, all as part of a plan to turn Storybrooke into the "New Camelot."

In Camelot's past, Arthur's obsession with Excalibur has taken a toll on Guinevere and leads to a betrayal of trust by Lancelot, as the two seek out the dagger. This leads to a confrontation with Rumplestiltskin, who offers a deal that Guinevere takes and ends up paying the price for at the hands of Arthur. This scenario comes full circle five years later, when Arthur learns of Emma being the Dark One from David after Mary Margaret confides that Lancelot is alive.

Unfortunately, David and Mary Margaret's plan to save Emma and help Lancelot is foiled with Arthur arresting Lancelot and using Guinevere to brainwash David and Mary Margaret into doing his bidding. Lancelot discovers that he is not alone in trying to stop Arthur, as he is joined by another cellmate, Merida. Meanwhile, Hook, with the help of Henry, tries to keep Emma from giving in to Rumplestiltskin's manifestations by spending a romantic day with her. Finally, in Storybrooke, Emma tells a reluctant Gold that she has plans to make him a hero and has found the perfect person to help her do the job: Merida.

In Camelot, Emma discovers how Merlin became a tree, so she and Regina race against time to find a tear of lost first love to release him, before Arthur stops them. At the same time Henry tries to prove to Violet that he can be heroic after confronting her father Sir Morgan, but a dinner date turns into a heartbreaker for Henry, which leads to his tear being used to free Merlin. Even as Arthur vows to get even, Merlin agrees to help Emma free her from the darkness.

In Storybrooke, Emma sends Gold and Merida into the woods so Gold can become the hero, but after seeing how cowardly he is, Merida takes the chipped cup and uses it to bring out his bravery. As Henry convinced Emma to help Violet look for her horse, Regina, Hook, Robin, and Belle sneak into Emma's home and discover not just Excalibur, but the dreamcatcher, where Regina discovers Violet's memories, in which Emma used her to break Henry's heart back in Camelot in order to obtain Henry's teardrop. Regina and Henry both feel betrayed by Emma and shut her out of their life.

In Camelot, Merida enlists Belle on a mission to save her brothers from the United Clans by using a spell to battle the clans, but Belle believes that her faith in fate should be enough to make Merida brave. In Storybrooke, Emma tries to force Merida to kill Belle so she can make Gold heroic.

When Gold finally realizes that Belle sees him as a coward, Gold brings out his bravery by defeating Merida after the archer turns into a bear. Gold then releases Excalibur and places it at Emma's feet but tells her that he is the hero now. At the same time Emma offers Zelena a deal while the residents discovers Arthur's deception, as well as discovering a message from Merlin with help from Henry.

In flashbacks, it is revealed that Merlin drank from the Holy Grail about 1,033 years ago, begetting his transformation into a wizard, able to heal the forlorn of his thriving village, he becomes a Christ-like figure. He meets a distraught woman by the name of Nimue, whose village and family were slaughtered by a mongol named Vortigan. Over time the two fall in love, but Merlin's immortality is an obstacle. They set out on a journey to forge the grail into a sword, that will cut away his immortality.

Using the Promethean Flame, Merlin conjures Excalibur, but Vortigan attacks them, apparently killing Nimue. However, Nimue had also drunk from the grail. Citing her newfound ability to take vengeance, she kills Vortigan, becoming the first Dark One, and breaks the sword into two pieces. Meanwhile, in Camelot, Merlin and Emma set out on a journey to speak with the first Dark One and claim the Promethean Spark; while Zelena double-crosses the heroes and joins forces with Arthur. Zelena imbues Merlin's name to the broken Excalibur, and Arthur uses it to command the suddenly enslaved Merlin to do his bidding.

In Camelot, after saving her family and friends from Arthur and Zelena, Emma struggles to rid herself of dark magic. She's holding herself back due to fear of commitment with Hook. She works through the fear and attempts to meld Excalibur, but Hook falls to the floor. Facing his death, Emma conjures the dark magic from the sword and instills it in Hook. He is reborn a Dark One. In Storybrooke, our heroes confront the treacherous Arthur. He gets the drop on Hook, but Emma swiftly subdues him.

She claims that all she's done has been for Hook then disappears. While Hook is in search of answers and a way to get Emma's attention, Zelena's pregnancy is suddenly expedited, giving birth shortly after. Believing Emma wants the baby, Regina and Robin rally defences, but she takes Zelena instead. Emma reveals her plan to transfer all dark magic to a vessel, Zelena, to rid the world of it forever. While she is away, Hook and Zelena escape. Zelena reveals to Hook one of Emma's dreamcatchers, enlightening him to his dark predicament.

Back in Camelot, Arthur is desperate for aid in his quest to unite Excalibur, leading him and Zelena to Dunbroch to find an enchanted helm. In flashbacks, it's revealed that King Fergus had gone to the wood-carving witch in the woods, asking for something that would ensure the longevity of his kingdom. She in turn gives him the helm. In present day Dunbroch, it's the day of coronation for Princess Merida. Just as she's about to be crowned, the witch appears and demands the helm be returned to her or she'll cast a bear spell on the entire kingdom.

On her journey, Merida recruits the aid of Mulan and Red, the former an old battle instructor for the princess. When they reach the helm, they are met with opposition from Arthur and Zelena, whom they and members of the clans overpower. Back at the castle, Merida declares she will destroy the helm instead of returning it to the witch. The witch explains that the journey was all a test to ensure that she had the necessary skills to lead the kingdom. The clans unite and Merida is crowned queen. Later, after speaking with the spirit of her father, Merida vows revenge on Arthur, who slayed him.

In Camelot, Hook embraces another path of revenge on the man he holds responsible for his life-long pain, Rumplestiltskin. Emma attempts to put a stop to his vengeance, but fails. She is then forced to take desperate measures. In Storybrooke, Henry and Emma team up to put a stop to Hook's Dark One misdeeds, while he is preoccupied with Rumplestiltskin. Meanwhile, Rumple and Belle experience relationship tribulations and Zelena adapts to skewed motherhood.

Back in the Enchanted Forest, Hook's feelings about his father abandoning him as a young boy lead to Hook killing him when Regina recruits him to kill Cora. In Storybrooke, as Hook and Nimue prepare to send Emma's family and friends to the Underworld to allow the resurrected Dark Ones to stay, his memories remind him of the man he wants to be.

When he realizes what will happen if he goes through with it, Hook turns Excalibur on the previous Dark Ones and asks Emma to sacrifice him with Excalibur, saving everyone and returning Emma to normal. Emma discovers Gold used the situation to tether the darkness back into himself, leading Emma to blackmail Gold into helping her bring Hook back from the Underworld. Meanwhile, Regina sends Zelena back to Oz, after Zelena attempted to get sole custody of her daughter.

The heroes arrive in the Underworld, which bears a striking resemblance to Storybrooke. Here, souls with unfinished business live, including Peter Pan and Cora. Cora offers Regina a way out, telling her she has one hour to leave on the ferry with Henry and Robin. Regina finds the soul of her father, whom Cora has threatened to send to a deeper layer of hell if she does not leave soon. When Regina's father tells her she has come too far to betray her friends now, Cora attempts to banish him.

However, as Regina has chosen to stay, Cora's attempts are ineffective, as seeing his daughter choose to stay a hero resolved his unfinished business. With his soul at peace, he is accepted into "a better place" and departs the Underworld after saying goodbye to Regina and Henry. The heroes realize they could potentially rescue all the souls here and continue their quest to find Hook with this in mind. Cora meets with the ruler of the Underworld, Hades, who wishes the heroes gone. He punishes Cora for her failure with an eternity as a miller's daughter once again. Flashbacks show Regina celebrating her birthday with a surprising visit from her mother, Cora.

After a prisoner is sent by Hook to tell Emma that he is alive, a creature known as Cerberus begins pursuing the outsiders. This prompts Mary Margaret to turn to the only person who can defeat the creature, Hercules, as she learns that he has unfinished business and is therefore in the Underworld. Back in the Enchanted Forest, he was responsible for giving her the courage to fight back against the Evil Queen's bandits. When the outsiders learn that he has lost that confidence, Mary Margaret decides it's time for him to restore it as they square off against Cerberus and, with the help of the prisoner, kill the creature, giving Hercules and the prisoner, revealed to be Megara, their tickets out.

In the process, Regina convinces Mary Margaret to again become Snow White, the woman who took risks before the original curse. A furious Hades vows to make the outsiders pay by forcing Hook to choose which living souls will stay behind as recompense for the souls they've redeemed. Meanwhile, Henry encounters Cruella, who wants him, in his role as The Author, to resurrect and return her to the world of the living, so that Emma's soul will no longer be branded a murderer's, but he keeps this offer to himself.

In the past, Rumplestiltskin is forced to promise his second child to a healer when Baelfire falls ill from a snakebite; however, after becoming the Dark One, he kills the healer to void the deal. In the present, Hades grows frustrated with Hook's refusal to chisel three names down onto the headstones, signifying those who will remain in the Underworld to replace Prince Henry Mills, Hercules, and Megaera. He threatens to drop Hook into the River of Lost Souls.

Mr. Gold finds Milah, the ex-wife he killed, convincing her to help him and Emma find Hook. However, while Emma rescues Hook, Hades offers Gold the chance to leave in exchange for destroying the boat; Gold blasts Milah out into the River of Lost Souls, hoping to keep the deal secret. Later, when Regina attempts to split Emma's heart in two to revive Hook, she finds a protection spell stopping her. It turns out Hades has chosen Emma Swan, Regina Mills, and Snow White to replace the souls they freed. Also, Hades reveals that he's taken on the debt Gold owes the healer; it turns out Belle is now pregnant. Now, Rumplestiltskin must now work for Hades; otherwise, Hades will take his unborn child.

In the past, Liam promises that he and Killian will find a way to get out of Captain Silver's servitude. However, he eventually gives in to Hades' offer of the "Eye of the Storm" jewel to buy their freedom, in exchange for selling out the souls of the entire crew during a dangerous mission for the same jewel. In the Underworld, Liam is reunited with Hook and joins the others in searching for the Underworld version of the "Once Upon a Time" book, only to be blackmailed by Hades who wants pages containing him removed.

When Emma catches on to Liam's deception, Hook learns the truth after Captain Silver and his crew reveal what Liam did in the past, which leads to Liam sacrificing himself to save Hook, allowing he and the ship's crew to move on. It is later revealed that the pages Hades wanted have something to do with Zelena. Meanwhile, Henry discovers that the Apprentice is in the Underworld to help guide him in finding the quill, hoping he will make the right decision in lieu of helping Cruella. Later, Cruella makes a move on David while he is impersonating James, only to realize the deception, and she tells David about James' resentment toward him, about being raised by their mother Ruth.

In the past in Oz, Zelena's plot to create a time travel portal is derailed by the return of Dorothy Gale. When Hades arrives to help Zelena with her plan to steal the Scarecrow's brain, the two find romantic feelings for each other but, after they succeed, Zelena turns on Hades, believing that he is using her in order to get even with Zeus. In the Underworld, Hades forces Gold to create a portal that brings Zelena, Belle, and Zelena's baby to the Underworld.

Unfortunately, when they arrive, Zelena discovers that Hades is behind the plot and that her magic is too weak to protect her child, while Belle learns the truth from Gold about his reclaiming his powers and her pregnancy, as well as the contract now with Hades. Zelena gives up her daughter to those who can better protect her, determined to keep Hades from using her to enact the time-travel portal, only to discover his love for her is unchanged. Meanwhile, Snow and David find a way to contact their son, and Henry starts to write stories in his sleep.

In the past, Belle meets Gaston, and they come upon a young ogre in the forest. Gaston wants to use violence to get information from him, but Belle believes there's a more compassionate way. In the Underworld, Hades enlists Gaston to seek revenge on Gold, leading Belle to find out his unfinished business, only to have Hades make a deal with Belle that could determine the fate of her unborn child.

Emma has a dream vision that comes true as she, Hook, and Snow attempt to reverse the graveyard spell. When Hook senses a storm brewing, he, Emma, Snow, and Regina go to the woods, where Emma uses her magic to take out the creature borne from the storm. The creature turns out to be a werewolf, who Snow discovers is Ruby/Red Riding Hood, having somehow ended up in the Underworld.

In the past, after teaming up in Camelot, Ruby and Mulan have made their way to Oz in search of the wolf pack. They meet Dorothy just as Zelena returns to Oz after being banished by Regina. Ruby and Dorothy form a bond as they work on a plan to defeat Zelena and get Toto back. In the present, Ruby finds herself in the Underworld after using a tracking spell to lead her to Zelena. Zelena reveals that she put Dorothy under a sleeping curse which can only be broken by true love's kiss.

The heroes believe that a kiss from Dorothy's deceased Auntie Em is the solution but, after Hades ruins their plans, Snow suggests to Ruby that her feelings for Dorothy might allow her to break the curse. Meanwhile, David and Snow get antsy after the phonebooth is removed and they have no way to check up on their son. After Hook is able to change the name on Snow's headstone to "David Nolan," Snow is able to leave the Underworld with Ruby and the two head over to Oz, where Ruby is able to free Dorothy.

Hades offers Zelena the chance for them to be a family, but at the cost of leaving the "outsiders" in the Underworld. Regina finds out about this and turns to Cora for help, leading to a bittersweet reunion and the possibility of closure. Meanwhile, David finally meets his deceased evil twin, James, who jealously decides to get rid of Emma and Robin with Cruella's help, using Zelena's child as leverage with Hades, but an attempt by David to everyone ends tragically.

Gold finds a loophole in his attempt to save Belle and kidnaps Zelena with help from Peter Pan. In the Enchanted Forest in the past, Cora brings Zelena from Oz to save Regina, only to have Cora end their reunion when they discover that they're related, because Cora fears Zelena's presence will derail Regina's future as the next queen.

In 2009 Maine, Emma buys food at Chantley's Lobster House while seeking her birth family. A bondswoman named Cleo Fox is after Emma for skipping town in Phoenix. At a nearby courthouse, Emma & Cleo are waiting for records from Emma's discovery as a baby, but find little of use. A year later in Boston, Emma is now a bondswoman seeking Cleo's biological daughter, Tasha, on behalf of her unexpected fallen friend.

In the Underworld, Hades, Zelena, her daughter, and the Storybrooke residents return home from the Underworld through a portal made by the fallen clock tower near the Underworld graveyard. The heroes all go through the portal except for Hook, who could not be saved in the end. With Hades' departure, Cruella announces herself as the new ruler of the Underworld.

As everyone returns to Storybrooke, they have to stop Hades, who wants to unleash the Olympian Crystal on those whom he sees as a threat. When Zelena's feelings blind her to the truth, Emma, Regina, and Robin have to find a way to prove Hades' deception, leading to Robin sacrificing his life for Regina and Zelena using the Crystal to destroy Hades. In the Underworld, a deceased Arthur, killed by Hades in Storybrooke, is joined by Hook to find the missing element in killing Hades.

After he succeeds in reaching Emma, Hook is allowed to move on, only to be rewarded by Zeus with a return to Storybrooke. Arthur stays in the Underworld as he was meant to repair a broken kingdom. Zelena names her daughter Robin in honor of her father during his funeral. Finally, after Moe refused to help bring Belle back from her sleeping curse and Hades chose not to make a deal, Gold takes advantage of the situation by acquiring a piece of the Crystal for a new plan.

Regina is mourning Robin Hood when Mr. Gold tethers all of Storybrooke's magic to the Olympian Crystal fragment in a scheme to awaken Belle. Because of all the pain magic has caused his family, Henry uses his Author powers to take the Crystal, intending to destroy magic; Violet teams up with him. Zelena opens a portal, allowing Merida, the Merry Men, and King Arthur's court to return to the Enchanted Forest; however, she, David, Hook, and Mary Margaret are sucked into the portal to the Land of Untold Stories, a place to where those who hated their lives chose to flee, where they are held captive by Mr. Hyde. In the meantime, Regina and Emma track Henry down to New York City, who is shadowed by Mr. Gold.

Henry finds a second, black-colored Holy Grail in the New York library, and uses it to banish magic during a fight between Emma, Regina, and Mr. Gold. He then learns, to his horror, that he has trapped the rest of his family in the Land of Untold Stories. In the Land of Untold Stories, Dr. Jekyll succeeds in separating himself from Mr. Hyde, wishing to join the heroes in Storybrooke.

After a pep talk from Emma, Henry gives a passionate speech to the people of New York about believing in magic, as their belief will bring it back; he convinces them to use magic wishes in the park fountain to help bring back his family. This opens a portal, bringing the heroes home and proving magic exists. Jekyll gives Snow some of his red serum for Regina, allowing her to separate from the Evil Queen and crush her heart. In the meantime, Gold has met with Mr. Hyde, who promises him information on how to wake Belle in exchange for Storybrooke. Hyde arrives in Storybrooke, along with some of his "friends," threatening the town. Back in New York, The Dragon is confronted by the manifestation of The Evil Queen, who takes his heart and declares war.