Our story begins in Neverland where young Baelfire has been brought aboard Captain Hook's ship, The Jolly Roger. The captain asks the boy his name and, while he finally replies, he makes his hatred of pirates pretty clear. He blames a pirate for tearing his family apart and killing his mother. Little does Baelfire know that said pirate is Hook himself! Hook, on the other hand, realizes that Baelfire is the key to his revenge against Rumplestiltskin as well as a final connection to his beloved Milah. Despite the creepy Lost Boys searching for Bae, Hook hides the boy, offering him sanctuary aboard his ship despite Mr. Smee's fearful objections. The Lost Ones and the one they serve are not to be trifled with.
In Storybrooke, Greg and Tamara activate the failsafe that will destroy Storybrooke. The forest begins to slowly reclaim the town and, when it's finished, anyone not from this world will be killed. Regina knows she can't stop what's happening, but she offers to do all she can to slow the process. That will give David time to get the magic beans back so everyone can use a portal to go back to The Enchanted Forest. Hook even offers his services, deciding it's better to live than to get his revenge. The only one not helping is Mr. Gold, who's so overcome with despair upon hearing about his son's likely death-Tamara shot him and he fell into a portal-that he's decided to wait for the end and do nothing to stop the impending doomsday.
David and Hook track Greg down to his hideout and confront him, but Tamara comes out of nowhere and shoots David, stunning him. Hook and Greg tussle over the beans and both end up with one before both sides go their separate ways. Everyone's ready to use the bean to get the heck out of town, but Emma's since learned that, by slowing down the destruction of the town, Regina won't be able to go with them. She has to stay behind and will be killed. Henry, Mary Margaret and David just can't accept that. They come up with a plan to send the failsafe and its destructive power into a void using the magic bean, but Emma and Hook aren't convinced it will work. Hook even tries to take the bean back, but Emma convinces him the others are right. Reluctantly, he hands the pouch with the bean back to her.
Emma, David, Mary Margaret and Henry go into the mines where Regina is busy using her magic to slow the destruction of the town. Already vines and trees are sprouting up everywhere, swallowing up the town. When Emma reaches into the pouch, she finds it empty. Hook pocketed the bean and is sailing off! Meanwhile, Leroy and the other dwarfs have a cure for Sneezy's memory loss from The Blue Fairy and they take his stein back from Gold's pawn shop. Leroy gives an extra dose of the cure to Gold, telling him he owes it to Belle to bring back her real memories, even if it is only to die. Mr. Gold initially decides against it, but in the end he can't help himself. He needs to spend his final moments with his true love. The potion restores Belle's memories and, once again, they're reunited.
Back in Neverland, Baelfire has begun to get comfortable aboard The Jolly Roger. He and Captain Hook bond over the fact that their fathers both abandoned them as children. Bae even confides in Hook about his father's dagger. But things go south when Baelfire finds a sketch of Milah on the Captain's desk one morning. Putting two and two together, he realizes that Captain Hook was the pirate who stole his mother away. Hook tells Baelfire the truth-that it was his father, Rumplestiltskin, who killed his mother. Even so, Baelfire wants off the ship. Hurt, Captain Hook turns Bae over to the Lost Ones, hoping to curry favor with the mysterious and apparently quite frightening Peter Pan.
In Storybrooke, the town is on the verge of destruction. Regina's not strong enough to stop what's happening, but Emma suddenly realizes that maybe the two of them are. Using her innate magic as the progeny of True Love, Emma adds her power to Regina's. Suddenly they're both blasted backwards and the failsafe falls harmlessly to the mine floor. Storybrooke is saved! Everyone is overjoyed, but as Emma looks to grab Henry for a moment of celebration, she sees he's gone. Greg and Tamara have taken him!
Greg and Tamara rush to the Storybrooke docks with Henry as their captive. They tell him they had come to town to destroy magic, but they had found something special that had changed everything-him! It seems whomever they're working for is very interested in him. Using their magic bean, Greg and Tamara pull Henry into a portal before Emma and the others can stop them. As they begin to despair, Belle notices The Jolly Roger on the horizon. Hook came back to help save the town, but, while he's too late for that, he's not too late to help Henry. He offers the bean, his ship and his services in recovering Henry. Emma, Mary Margaret, David and Regina all climb aboard. Mr. Gold tearfully says goodbye to Belle-he must honor Baelfire by rescuing his grandson. He leaves her instructions on how to once again cloak Storybrooke from outsiders.
Aboard The Jolly Roger, Hook agrees to quit trying to kill Gold. Gold, in turn, produces the magic globe he received as a gift from Cora. Using it, they track Henry down to Neverland. Gold suddenly figures out who Greg and Tamara have really been working for and he warns everyone that it's someone they all should fear. Hook tosses the magic bean into the water and The Jolly Roger sets sail, sinking into the portal to Neverland!