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We started with the Author, who is selling televisions, badly it seems. He can't even sell 'em with the new color feature or "with the clicker" in December of 1966. Ironically, Isaac - the real name of the Author -- is trying to make it as a writer when he gets a letter from Star Publishing inviting him for a meeting.
The Sorcerer's Apprentice is the interviewer. He tells Isaac to "choose one" as writing utensils are laid before him. It's a test to see what kind of writer he is. Isaac picked the correct quill, and he is introduced to his destiny when the Sorcerer's Apprentice opens a magical door out of thin air, and he can see it.
As we see Isaac's beginning, we see the heroes frustrated, looking through shelves of empty magical storybooks for ways to stop him. Regina and Hook fear what Rumpelstiltskin will have Isaac write -- what story he will cast them in. Emma calls in August, who knew the most about the Once Upon a Time book. With his help, they find that they need the Sorcerer's Apprentice -- whom Hook has seen before. He banished him, while under the Dark One's influence, into the Sorcerer's hat. It's OK, though. The Blue Fairy is able to pull back through the Sorcerer's hat, keying in on him by using his iconic broomstick. And now, they go after Isaac and Rumpelstiltskin.
Isaac has been busy writing, and the duo are crafting happy endings in a new book. Isaac could make Rumpel forget Baelfire/Neal, but Rumpel is against that. He wants Bae to have seen him as a hero.
As the heroes close in on them, Isaac is quicker with the quill. He finishes his story with a seemingly final "The End." The magic of the book does its things, and life as the denizens of Storybrooke know it drastically changes.
Henry, knocked out by the powerful magic, wakes up as seemingly the only person left in Storybrooke. He finds a solitary record player in Mr. Gold's shop that is still playing, but no people. So what do you do in a ghost town with no people? You steal a car and go to another town. In a diner down the road, Henry sees a book in the spinner rack called "Heros and Villains" that has Isaac's picture on it.
Isaac has crafted himself a good life. He's a successfully writer with many fans, it seems. His popular book is about "what happens when villains win the day." Henry finds Isaac giving a chat on villains winning the day. During a book signing, we find that fans seem to love Regina -- as do we all.
Isaac has put them all in the "Heroes and Villains" book. Everyone's ending was rewritten, except Emma because she was never really part of the story, but she is in the book. Henry threatens Isaac, but Isaac has no power to undo what he did. But Henry, with the key, is able to go into the new storybook and will of course try to be the hero and save his family. Isaac, though, has followed him into the book and knocks Henry out.
A now chained Henry faces death in the form of a rampaging ogre -- thanks to Isaac. But Rumpelstiltskin the knight saves him using light magic. He doesn't at all remember Henry and tells him to be on his way. Yep, the roles are flipped.
Along the lines of role reversal, Regina, she of the regal gowns and ornate headpieces, is living in the forest. Henry is able to find her because he kept a copy of the book that Isaac wrote, which leads him to Regina. Of course, as soon as they meet, she points a bow and arrow at him. He tells her the whole story, but of course she doesn't believe it. He tells her about Operation Mongoose and the whole plan to find her happy ending. Regina throws the book in the fire. Darn, thought he'd be able to use that as a road map. Argh.
Isaac gets caught up in a trap. The evil dwarfs capture him for the evil queen: Snow White. Decked out in in black and silver, a cruel-hearted Snow White has the heart -- the actual heart -- of Prince Charming, and orders him to kill Isaac. But Isaac talks himself out of it by mentioning Charming's twin brother, James, whom Snow had apparently loved. He promises to help Snow White find and get revenge on Regina, who somehow wronged her in this world. In return, she must kill Henry. It's a deal.
Snow and Regina do confront each other when Snow catches Regina trying to rob a carriage, which Isaac the Author no doubt knew about. Regina even read about it in a book -- that should've thrown her off, at least, but anyway. The Snow-Regina relationship is a mirror image of how they treated each other when the roles were reversed. Regina had a hand in the death of James (Charming's brother), and Snow is about to burn her up in a fireball when Robin Hood rides by and saves the day.
Robin, who is actually her rival in thievery, offers her the leadership post of the Merry Men, as he's going to turn his life around. She refuses and thinks that there may be romance in the air -- but once again, Zelena the Wicked Witch steps in the way. She is to wed Robin. Even in the mixed-up Heroes and Villains world, Regina can't find her happiness! Dang.
Regina tells Henry that he should find his other mother and then remembers that Emma -- calling herself the savior -- was put away in a remote prison by evil queen Snow White. Henry's now on a quest.
Isaac is also on a quest -- to keep his happy ending. So he finds Rumpelstiltskin, who is married to Belle and with children, and tells him that he has to kill Regina and keep her from her happy ending or his perfect life will crumble. The world will know him for the coward that he really is, even though he has been rewritten as a hero. Somewhere deep down, Rumpel can tell it's true.
Henry finds Hook and the Jolly Roger, but he's not the Captain. Blackbeard is in charge, and Hook is a scared deckhand who doesn't want to act. Topsy-turvy world. Henry knocks out Blackbeard with a heavy pulley, and they dump Blackbeard while taking the ship to find Emma. Henry helps Hook sail the boat -- mostly because Henry was taught how to sail by Hook himself, who doesn't remember that. Once they get to the island where Emma is being held, Henry knocks out the guard -- ummmm -- and goes to find his mom.
Lily was the guard! Still, Henry the teen knocked her out? Oh, well. Henry rescues Emma, and they all jump back on the boat to escape. It's not a smooth getaway, though, because Lily wakes up and turns into a dragon. She goes after the trio but is shot out of the air by Emma as she tries to pursue them.
Lily's not done, though. As Emma and Hook and Henry relax, Lily leads evil Snow White right to them. They fight, and though Hook had the upper hand on a bewitched Charming, Charming gets up and kills him after a distraction from Snow White. "I never did like pirates." Emma is devastated, but she and Henry have to run as Snow hurls a fireball at them.
Belle and Rumpel talk about the revelation that the Author gave them -- that Rumpel was actually a bad guy masquerading as a good guy. Belle talks Rumpel into being the hero that she believes him to be -- but it may be falling on deaf ears.
Henry takes Emma to Regina, and Emma tells Regina that she has to tell Robin that she loves him, which will help end the book and revert people back to normal. Emma, with tears in her eyes, tell Regina that she just watched the man she loves (Hook) die, and she never told him that she loved him.
It's convincing enough. Regina, Emma and Henry crash Zelena and Robin's wedding -- but Rumpelstiltskin is there to stop them.
As Emma fights -- swordplay! -- Rumpel, Regina is mustering the courage to bust in on Robin's wedding to Zelena to tell him she loves him. Rumpel gets the upper hand and knocks Emma out. Henry picks up a sword to defend his mom, but he's no match. As Rumpel is about to behead Henry, Regina steps in to take the fatal blow, a gash to the stomach.
Isaac comes in and is happy with Regina's impending death. Robin and Zelena excite the church, happy in the new marriage, but Robin runs to Regina once he sees that she's mortally wounded. He tries to help her, which causes jealousy to well up in Zelena, and a tinge of the Wicked Witch's green skin unveils itself. She runs off before a full transformation can happen. That would've been something to see them all there!
The bells begin to toll, signaling the end of the story, and a return to the way that Isaac wrote the the tale to be.
Henry, though, picks up the magic pen -- the one that only an Author can wield. He's the new Author! Isaac is not worried because there's no magic ink, and only the blood of a savior can help write the story. Henry thinks fast, and using Regina's heroic sacrifice, and her blood, he is able to rewrite things to go back to the way that they were -- returning everyone to their true selves and placing them back in Storybrooke.
Everyone's relieved to be home, and there's a party going on at Granny's!
Emma tells Hook that she appreciates him for all that he's done.
Regina relays that Zelena is still locked up and still pregnant, but she and Robin will get through it. A rekindling?
Isaac is caught by Snow and Charming as he tries to get away. He blamed his wrongdoing on a lifetime of bad bosses, who, like Charming and Snow, made themselves seem better than everyone else. Snow says that Isaac became a villain when he put his own desires above everyone else's.
Henry is schooled by the Sorcerer's Apprentice in the power of the Author and his new responsibilities. He can remake lives and create new ones, but he can't change what's been written because it is "the truth." Henry says "No one should have that much power," then he breaks the magical quill. The Sorcerer's Apprentice is happy to see it.
Leave it to Rumpel to break up the good times. Belle goes to Rumplestiltskin's side as he's dying. He never believed that anyone could ever love him, though he did really lover her. She doesn't love Will and still loves Rumpel. But he's dying nonetheless, and she needs help.
Belle interrupts the merriment at Granny's and asks for help with Rumpel. The heroes, including the Sorcerer's Apprentice, head over to Mr. Gold's shop to do what they can. The Apprentice attempts to take the darkness from Gold, which should help his heart heal. But the darkness can't be contained by the Sorcerer's hat and has to be housed in a person. When it escapes, it goes after the Apprentice, but Emma drives the darkness out with her own light magic. it escapes.
The Sorcerer long ago battled the darkness and is the only one who could hold it. To do so, he had to put it in one person/vessel, and that created the Dark One. When the Sorcerer's Apprentice tries to help Rumpel, he releases it. The Sorcerer's Apprentice says they'll have to find the Sorcerer, whose real name is Merlin!
Knew that, right? Anyway, as the heroes look for it, wouldn't you know, the darkness goes right for Regina. Can she get a break?! As it tries to strip Regina of her good, Emma takes on the savior role once again. She can't let all of Regina's hard work go to waste, and after kissing Hook and telling him he loves her, and imploring her parents to help fight the darkness inside of her, she reaches into it and takes the darkness into herself.
The last image we see is the savior rising into the air, darkness swirling around her, and the dagger of the new Dark Lord dropping. On it reads Emma Swan.