When Emma breaks the Dark Curse, Neal resides in New York City, where he receives a postcard delivered by a dove. One side of the postcard reads, "Broken", and the other is a photo of the Storybrooke Clock Tower with the phrase "Greetings from Storybrooke", which is sent to him by August. ("Broken")
Neal receives a call buzz for his apartment room one day. When the person on the other line says there is a UPS delivery for him, for an unknown reason, he flees out the window and down the ladder escape. He runs away from his pursuer until they both careen into each other and knock heads. Neal is stunned to see the person chasing him is Emma. She accuses him and his father, Mr. Gold, of deceiving her. Not wanting a confrontation out in the open, Neal succeeds in getting Emma to a nearby bar where he reveals that he is, in fact, Baelfire and they discuss their past. Neal makes note of the fact she is still wearing the necklace he gave her, but Emma takes it off just then and hands it back to him. He suggests that they go their separate ways and that she tell Mr. Gold she lost him. Although Emma agrees, Neal decides to go back to his apartment as he knows what his father does to people who break deals with him. He stops Mr. Gold from threatening Emma and commands him to leave, but feels confused when he sees Henry, who he does not recognize. When Emma states Henry is her son, Neal admanantly demands to know how old he is. Henry shouts back he is eleven years old, which is the exact amount of years since he and Emma were together. He realizes the boy is his son. Mr. Gold blackmails Neal into talking with him as that is the only way to fulfill Emma's bargain. Neal tells Mr. Gold that since he himself as an abandoned boy never got closure, neither will his father. Emma allows Neal to get to know Henry, but warns not to break his heart. ("Manhattan")
Some time later, Neal is building a quick relationship with Henry by introducing him to New York-style pizza and promising to take him to a museum. Neal tries to tell Emma something important, but their conversation is interrupted. Neal and Henry head back up to the apartment room to fetch a camera for the museum visit only to rush back to see Mr. Gold has been stabbed by Hook, who Emma has already knocked out. To everyone's surprise, Neal admits he is already acquainted with Hook. Mr. Gold tells Emma the wound inflicted on him by Hook contains poison and the only way to cure him is with magic in Storybrooke. Realizing that Hook's ship is the fastest way to get back, Neal offers to steer the ship and arranges to borrow someone else's car to the harbor. Emma curiously asks how he knows Hook and how to pilot a pirate ship, though he evasively says the land without magic is not the first world he arrived in, because if it had been, he would been over three-hundred years old by now. When they arrive next to a large car, Neal prepares to use the keys when the owner of the vehicle, his fiancée, Tamara, walks up to greet him. He introduces Emma to his future wife. ("The Queen Is Dead")
Neal pilots the Jolly Roger from New York to Storybrooke with the aid of Henry. While en route, Emma telephones David and Mary Margaret, to fill them in on what has happened. David explains to them Cora and Regina have possession of the dagger which can be used to control Mr. Gold. They arrive at the pawnshop, and once inside, Mr. Gold gives a piece of magic invisible chalk to Emma and tells her to draw a magic barrier across the door with the chalk. Neal jokes that he did not know she could use magic, and Emma chides at him for not telling her about Tamara or who his father is. When Cora and Regina reach the shop, they use magic to break the barrier, and end up battling Neal, Mary Margaret, David and Emma. Regina ejects David by throwing him out of the shop. After distracting Cora and Regina, Emma proceeds to draw another barrier outside the shop's back room to protect herself, Neal and Mr. Gold for a little longer. After hearing Mr. Gold's emotional phone conversation with his girlfriend Belle, Neal realizes that his father has changed. In that moment, Neal is still embittered about the past, but still loves his father. They are interrupted by Cora breaking through the barrier. Though Neal and Emma rise to defend Mr. Gold, she teleports the two away to the town forest. ("The Miller's Daughter")
After Cora's death, Mr. Gold visits the apartment to warn Emma and David about what Regina has planned for Mary Margaret. Henry is horrified about his family's possible intent to kill Regina to end the feud. Emma takes an upset Henry to the diner where Neal hangs out with him. He orders him a nice dessert, but Henry knows Neal is in on trying to sweeten him up so he does not try to get involved with Regina. Neal asks Henry to move to New York with him where he will be safer. Henry agrees, and then goes to the bathroom. Emma comes back to check up on them, and is incredulous that Neal fell for the "I'm going to the bathroom" trick; especially since Henry took his backpack with him. They try to catch up with him, and get to the mines with help from Ruby and realize Henry took dynamite to blow up the wishing well to get rid of magic. They hurry off to the well, and nearly have a heated battle with Regina, but Henry manages to get everyone to stop. Henry convinces Regina to not use the spell on him, and she willingly burns the paper. ("Welcome to Storybrooke")
Henry and Emma pay a visit to Neal at his guest room at the bed and breakfast. While Neal sends Henry off to the diner and order three hot cocoas, he finds the time to tell Emma that Hook has escaped from the storage closet, and Tamara is coming to Storybrooke. Emma does not like the idea of another outsider in town, and tells Neal he should tell Tamara his true identity. The foursome have an awkward breakfast in silence, but the conversation picks up when Henry asks how the two of them met, to which Tamara briefly relates the story. Once Henry and Emma head off to elsewhere, Neal shows Tamara the book and tells her about his life in the Enchanted Forest; stating all the fairytales in the book are real. Perceiving this is a ploy to drive her away so he can get back with Emma, Tamara expresses anger and frustration at his story, and storms out. Later, in front of the sheriff department building, he witnesses a wooden August die with his last words warning Emma about "her". After Mother Superior arrives and transforms August back into Pinocchio, Tamara arrives to see the workings of magic and realizes Neal is telling the truth. She decides to stay in Storybrooke for Neal. ("Selfless, Brave and True")
In the park, Neal and Henry have fun playing with wooden swords. At the end of the day, he brings home a worn out and asleep Henry. Emma tucks him into bed and then the two sit down to talk. She casually asks him if he would go back to the Enchanted Forest if there was a way, but Neal states he spent his whole life running from it. ("Lacey")
On a rainy day, he and Tamara huddle under an umbrella as they are leaving the bed and breakfast. He returns to the guest room to find Henry waiting outside. As Henry struggles for a reason for his appearance, Neal notices that he is kicking the door. Recognizing the door tactic as his own, he bursts into the room to find Emma prying open a loose floorboard. Emma explains her suspicion of Tamara as possibly being the person August was warning them about. She also harbors doubts since Tamara has a list of everyone in town and their fairytale names, though Neal replies he gave that list to her so his fiancée can come to grips with Storybrooke and his identity. Neal goes out on a limb and allows Emma to open the floorboard, but nothing incriminating is found in it. He asks Emma whether her reluctant behavior is due to Tamara being in Storybrooke. She strongly denies it and leaves with Henry. ("The Evil Queen")
Neal awakens in bed to see Tamara dressed and ready to go on a marathon training run. He tries to persuade her to sleep in, but she reasons the training is necessary so she can be prepared for the upcoming marathon. Emma confronts Neal with the news Regina is missing and goes back to pointing the finger at Tamara. Neal is still very much in disbelief even when Emma notices sand on the floor left by Tamara's shoes, which indicates she has not recently been running in the woods, but near the beach. He follows Emma along to the shoreline where Tamara casually jogs up. She explains to Neal the reason for her change of jogging spots from the woods to the beach; an answer that satisfies him. After Tamara leaves, Neal tries to be sympathetic to the difficult time Emma is having in his fiancée being in town. Emma fights against his accusations that she is in any way jealous of his current relationship. When she tries to walk away, he spills out the truth about wanting to go back for her when she went to jail in his place. Neal admits he truly wanted to, but was too scared to face Emma thinking she might never forgive him as he never forgave himself for leaving her.
After figuring out Regina is trapped in the town cannery, Neal and Emma head inside the building. Via phone, David warns Emma to be on the lookout for Greg as he is trying to escape the building. Neal is relieved to hear Tamara is not involved, but his ease turns to horror when Emma unexpectedly is knocked out unconscious by her. To his shock, Tamara fully admits to lying about everything since the day they met. Though she thinks he is a good man, her job is more important. She shoots Neal in the abdomen and apologizes, though Emma kicks the pistol out of Tamara's hands. Tamara distracts them further by opening a portal. Emma almost falls in, but is pulled up by Neal. Then, Neal ends up clinging onto Emma to keep from falling into the portal. Neal urges her to let go, but Emma is more concerned that he'll die from the gun shot wound no matter what world he lands in. Terrified of losing him, she confesses her genuine love for Neal. He reciprocates his love for her and then disappears into the portal. ("Second Star to the Right")
He lands in the Enchanted Forest by the shoreline of the beach. While unconscious, three strangers, Prince Phillip, Aurora and Mulan take him back to the palace and tend to his injuries. Awakening on a bier, Neal is met with the watchful stare of Mulan. She asks who he is, and Neal responds with his name. Her companions, Aurora and Prince Phillip, rush over. Neal learns he is back in the Enchanted Forest. Aurora thinks he is a native of this land, but Mulan points out his clothes are foreign and similar to Emma and Mary Margaret's. At the mention of Emma's name, Neal informs them that he must save her. His wound is not yet completely healed, but he mentions a need to make sure Emma and Henry are alright. Aurora, having previously met Henry in the Netherworld, promises to look for him there again. As they wait for Aurora as she searches, Neal and Mulan converse. He explains that after falling into the portal, his thoughts focused on the Enchanted Forest, which brought him back. Aurora's attempt at contacting Henry is unsuccessful, so Neal goes to his father's old castle to find an item for reaching Emma and Henry.
Neal and Mulan go on foot towards the castle. Wishing to learn more about Neal's relationship with Emma, she asks why Emma never mentioned him before. Neal confesses he broke Emma's heart by letting her go to fulfill the breaking of the Dark Curse, and after it was finished with, fear of rejection kept himself from coming back to her. Mulan remarks that his belief in love wasn't strong enough to overcome rejection, which Neal says is the greatest regret of his life. Inside the castle, a man, Robin Hood, aims an arrow their way, and claims the castle is his. Neal explains the castle once belonged to the Dark One, Rumplestiltskin, and he is his son, Baelfire. Robin Hood decides to trust Neal's words and mentions being indebted to Rumplestiltskin for sparing his life in the past. After looking around for a bit, Neal picks up his father's old walking stick and swings it around to activate a hidden door. He shares knowledge of his father's enchantment of the walking stick with blood magic that only allows the caster or those of his lineage to be able to use it. From within the door, Neal discovers a crystal ball and attempts to activate it by touch, which causes no change. Mulan suggests thinking about how he feels about Emma as a guide. Neal follows her instructions, and the crystal ball shows him an image of Emma in Neverland. ("And Straight On 'Til Morning", "The Heart of the Truest Believer")
Panicking over finding another pathway to Neverland, Neal searches all over for something that could be of use, but to no avail. Just then, four of Robin Hood's allies from their group, the Merry Men, enter into the castle. From beneath the leading man, Little John, a four-year old boy, Roland, crawls out and runs into Robin Hood's arms. He finds out the child is Robin Hood's son, to which he suddenly comes up with the idea of how to traverse worlds. Neal suggests Roland can use a summoning incantation to call the Shadow so he himself can gain a pathway to Neverland. Once Robin Hood learns the Shadow is notorious for snatching away young boys and whisking them away, he is extremely resistant to the idea. However, Neal reminds him how his father saved Robin Hood's wife, which allowed her to give birth to Roland, and as such, this makes him in Rumplestiltskin's debt. Robin Hood finally relents in his decision. Roland summons the Shadow, who attempts to pull him away, but Mulan severs one of its arms. Neal quickly latches onto the Shadow and is flown back to Neverland. After a rough landing, he is greeted by Felix. The Lost Boy welcomes him home, and promises Pan will be very happy to see him. ("Quite a Common Fairy")
With his wrists bound, Neal is forced to trail behind Felix through a trek in the jungle, but begins to undo his restraints without the Lost Boy noticing. At the right time, Neal ambushes Felix, rendering him unconscious, and then makes a run for it. He sprints straight into a stranger wielding a spear. Upon stopping, he realizes, in bewilderment, it's his father, Mr. Gold, who begins accusing him of being a mirage. Neal tries to explain that he's not dead, but Mr. Gold believes he is an illusion to reminder of his failures and make him question the decision to save Henry. As Mr. Gold prepares to kill him, Neal chokes out a plea by calling him Papa. This causes Mr. Gold to loosen his grip. Neal is brought up to speed about the last time his father saw Emma when they were heading to the island on Hook's ship. Mr. Gold doesn't believe Emma has the stomach to do what must be done and thinks Neal is the same. He begs to differ and learns his father is actually serious about giving up his own life for Henry. Neal has a better idea, however, and kills a colossal squid by the lake so Mr. Gold can extract squid ink from it. They storm into Pan's camp after Mr. Gold puts all the Lost Boys as well as Henry to sleep. Neal shoots an arrow at Pan, which is coated at the shaft with squid ink. As suspected, Pan catches it in his fist; paralyzing him. As they make off with a slumbering Henry, Pan tells Neal of a prophecy that Mr. Gold wants to keep from happening by murdering Henry. Neal later demands an explanation from his father. With much reluctance, Mr. Gold acknowledges that the prophecy spoke of a boy, presumably Henry, who will help him find Neal, but ultimately is his own undoing. Despite his father's insistence this was before he discovered Henry is his grandson, Neal begins to lose trust in him. As proof Mr. Gold changed from the past, Neal asks for the Dark One’s dagger. Though he swears the dagger is hidden in a place not even he knows where, it sounds like another empty excuse to Neal. Too afraid his father will go back to his old ways, Neal purposely presses a leaf coated in squid ink into Mr. Gold's palm. While doing so, he brings up a childhood wish of his father coming to save him from Neverland, but realized it was never going to happen since the dagger is more important to him than his own son. While Mr. Gold is paralyzed, Neal leaves with Henry, despite his father's warning that he won't he safe without the protection of magic. On his own, Neal comes to a deserted campsite he believes was recently inhabited by Emma. Pan and the Lost Boys take him by surprise to steal Henry back. When reminded by Pan that no one walks off the island without his leave, Neal boasts he already did once. Pan attests that everyone is exactly where he wants them to be. At the sound of Henry groggily waking up, Pan ushers some of the Lost Boys to take Neal away to an unknown holding location. ("Nasty Habits")
Drugged and placed in a cage, Neal slowly drifts into unconsciousness when Pan arrives to check up on him. On his orders, the Lost Boys hang the cage up next to another confined prisoner. ("Good Form")
At another time, Neal, while still in the enclosure, is brought into an Echo Cave as bait for rescue on a platform. He awakens to see David, Emma, Hook and Mary Margaret standing at the other platform end of the cave. Separated by a gaping space between the two sections, Hook, Mary Margaret and David all satisfy the requirements of the cave by revealing a guarded secret about themselves, causing a bridge to form, allowing Emma to cross over to Neal. Emma attempts to cut Neal free, which is all in vain, when he implies that she, too, must also follow the cave's requirement. With reassurance from Neal, Emma tearfully acknowledges that she still loves him since the day they met again, but had hopes he wasn't alive because their relationship has given her a lot of pain and she just wanted to move on. The cage bars melt away as she and Neal embrace each other. When they reach the outside, they decide to regroup with Tinker Bell first and then continue the mission. Left alone with Neal, Emma is sorry about what she said to him earlier, though her feelings cannot be changed. Neal doesn't believe she has anything to apologize for, but affirms he won't stop fighting for her. ("Ariel")
Neal familiarizes the group on a tactic for flying off the island using Pan's shadow. Since the Shadow is mostly solitary, they can capture it without going near Pan. Emma steps up on "shadow duty" with Neal as Hook enlists himself as well. They all agree to meet back at Tinker Bell's tree house once the Shadow is nabbed. Neal, Emma and Hook revisit the Lost Boy cavern. While Emma goes off to fetch the star map, Hook accidentally discloses the kiss he shared with her, which Neal was unaware of until now. This causes some uneasiness in Neal, but he excuses it as something Emma must've forgotten to bring up. Next, they go in search of Dark Hollow, which is home to all captured shadows. On the way there, Emma lends Neal a weapon to cut through tall grass. Neal recognizes it as his old cutlass, and after learning Hook gave it to her as a memento, he angrily snips at the pirate before walking away. After heading into Dark Hollow, Neal briefs on drawing the Shadow in by lighting the candle and trapping it by putting the lid on. He and Hook end up fighting over the lighter when three shadows show up to attack just as Emma grabs the coconut halves. Both men are thrown against trees and begin having their shadows ripped out. Emma saves the day by using magic to light a flame on the candle and entrap the Shadow inside. On the journey back to Tinker Bell's tree house, Emma settles the competition between Hook and Neal by stating the only person she is choosing is Henry. After showing Tinker Bell proof of the Shadow as their ticket off the island, she agrees to do her part in taking down Pan. Emma stays behind with Neal, who calmly accepts what she said earlier and thinks of Henry as the best thing that came out of them being together. She agrees. ("Dark Hollow")
While moving ahead to Pan's camp, a rustle from the jungle causes the entire group to assemble for battle, but it turns out to be only Regina and Mr. Gold. Regina tells them about the power of Pandora's Box while Neal's distrust reaches a pinnacle. He blurts out Mr. Gold's objective to kill Henry and prevent a seer's prophecy from coming true. Subsequently, Emma and everyone else turns against Mr. Gold by drawing their weapons. To keep him at bay, Neal forces his father to hand over the box and warns him against using magic. As they all file past to continue on, Neal cautioned by him about underestimating Pan's power. He tries for an answer concerning his father and Pan's history together, but Mr. Gold remains silent. Later, Mr. Gold offers his services to make an elixir so David can be out of Neverland's waters without dying. The catch is, as usual, his father wants a favor out of the deal, which Emma is willing to partake, but Neal can't stomach it. He strikes down the asking price by pushing Mr. Gold to help for the right reasons rather than for his own personal gain.
After Tinker Bell gains access into the perimeter of the encampment and the Lost Boys are put to sleep by Regina, neither Henry or Pan are found there. Instead, Neal frees an old friend, Wendy, and brings her back to camp to inquire about Henry. Forced to act on Pan's wishes, Wendy lies to them. Mr. Gold calls her out for not telling the truth. With some encouragement from Neal, Wendy opens up about Pan's real reason for needing Henry's heart, which is to save himself from dying and then become immortal. As a trade, Pan lives, but Henry will die. By rowboat, Neal, Emma, Mr. Gold and Regina ascend onto Skull Rock to stop Pan. Instead, they are stopped by a barrier, enacted to keep out anyone with a shadow, blocking their path up the stairs. As Mr. Gold is the only one without a shadow, he is able to enter through. This fact surprises Neal, who had previously thought he was lying about ripping away his shadow. The box is handed over to Mr. Gold, but while he is gone, Emma and Regina use magic to block out the moon as well as their shadows. The trio rush up to the upper level to witness Henry pulling out his own heart. All three attempt to dissuade him from the sacrifice, but through Pan's manipulations, Henry chooses to give up his heart. They cry out in horror as he plunges the heart into Pan's chest, causing all of them to be thrown back from the impact, and Henry collapses. As they rush over to check up on his unmoving body, Pan rises into the air. ("Think Lovely Thoughts")
Before Pan flies off, he reveals Mr. Gold is now powerless and trapped in the box. Neal proposes they look for Pan at the Lost Boy camp, though Regina lashes out over the ridiculous idea since their nemesis wouldn't risk going back there. Unable to come up with a plan, they bring Henry's body back with them to the Lost Boy camp where Regina casts a preservation spell on him to last one hour until they track down Pan. Emma manages to get some of the Lost Boys to open up about Pan's current location at his "thinking tree" in Pixie Woods after promising to bring them off the island. While Emma, Mary Margaret and Regina go to find Pan, Neal and the rest of their party plan to regroup aboard the Jolly Roger. The three women come back in time to place the heart back in Henry as he gasps to life. Additionally, the box has also been retrieved and given to Neal. He is astonished by find out Pan is actually Mr. Gold's father. After releasing his father from the box, the two make up over their past differences and problems. Neal sees his father truly cares about the well-being of Henry, and feels badly for not believing in him. Mr. Gold expresses fears that he turned out just like Pan by leaving his own son and being selfish. Though Neal has always held a grudge against his father for that abandoning him, he now recognizes Mr. Gold has changed for the better. Home bound, Neal releases the Shadow over a lit cannon, firing the creature into the air, to which Regina projects it into a sail to fly everyone home. ("Save Henry")
Following a safe journey out of Neverland to Storybrooke, Neal is given a shot to court Emma after Hook resigns himself to step back for Henry's sake. Immediately, he uses the opportunity to ask Emma out for a low-key lunch at the diner. The following morning, Emma doesn't show up, to Neal's disappointment. Trouble once again arises in town when the Shadow kills Mother Superior. After regrouping with the others, it is suspected Pan is behind the attack. Neal, Hook and Tinker Bell go to fetch the lighter and coconut halves from the ship in case they need to catch the Shadow again. They attempt to enter the vault where Regina took Henry to keep him safe, but the door is locked. Belle, Emma, David, Mary Margaret and Mr. Gold bring back Pan, who is actually Henry, since the two switched bodies. When Mr. Gold breaks open the vault, they discover Pan took the spell for the Dark Curse. ("The New Neverland")
Mr. Gold shares with everyone of the only viable way to stop Pan's curse is for Regina, as the original caster of the Dark Curse, to undo it by destroying the scroll, though there will be a steep price for this. They plan to switch Henry back to his own body so he will be in possession of the scroll and bring it to Regina. Mr. Gold can perform the spell, but needs a strong outlet in order for it to work. Tinker Bell has knowledge of a powerful Black Fairy wand that Mother Superior kept. Neal, David, Hook and Tinker Bell ask the convent nuns for the item just as the Shadow attacks. On Neal's urging, Tinker Bell uses her vial of pixie dust to light a flame on the coconut half and flies into the air to trap the Shadow; disposing the being for good by burning it in a fire. With the Shadow gone, Mother Superior returns alive and hands the Black Fairy's wand to them. The three men arrive at the pawnshop with the wand. Once Henry's spirit returns to his own body, everyone except Mr. Gold runs off to find the boy. With Granny's tracking skills, they reunite with him. Regina passes out after taking the scroll and awakens with knowledge of the price for stopping the curse. They are accosted by Pan as he steals back the scroll and freezes them in place. Pan chooses Neal as his first kill when Mr. Gold shows up. Mr. Gold summons the dagger and stabs Pan as well as himself with it, killing both of them, while Neal watches in shock. After learning the price of stopping Pan's curse is all former Enchanted Forest inhabitants must return to their old world, Emma and Henry will leave town together while Regina crafts new memories for both so they forget everything. Before this, Neal says goodbye to them with the promise they will see each other again. As the two cross out of Storybrooke, Regina stops the curse from taking over as everyone inside the town is sent back to the Enchanted Forest. ("Going Home")