In the first hour of the special two-hour season finale, Everyone is mourning the death of Robin Hood. As shocked as she is to see that Hook is alive, Regina realizes that she needs to deal with whatever Mr. Gold is planning after a magical blast rocks Storybrooke. She takes offense at Emma's request to sit out this next battle. She'll deal with Gold and the tethering spell he's using with the surviving piece of the Olympian Crystal and wake Belle on her own.
Henry reunites with Violet. He tells her about how magic has hurt so many people. Violet has felt the pain of this as well. The two of them make plans to go on a quest to fix things. Henry uses the author's pen to take possession of the Olympian Crystal. The plan is to take it out of town and destroy it once and for all. Rumple tells the heroes that, if Henry succeeds, he'll unwittingly destroy all of Storybrooke, too. He's off to find his grandson. Regina reluctantly teams up with Emma to get to him first.
Henry hid his phone on a bus headed to Boston to throw his GPS-tracking moms off his trail. Emma and Regina realize their magic now works in the real world. That means Gold's does, too. They have to find Henry and Violet, who have made their way to New York City. They are looking for Neal's journal. Its pages may have a way to destroy magic.
While on the hunt for Henry, Regina finds a letter that Robin wrote to her. It's a sweet note. It leads to Regina admitting that the Evil Queen is still inside her trying to get out. She's constantly to at war with her instincts. She hates doing good because it always leads to loss with her. Regina believes that she's trapped to live a life where her past evils will always haunt her.
Word gets out around town that magic may disappear. Zelena opens up a portal door to allow those who want to leave town for Fairy Tale Land before this happens. Snow, David, Hook and Zelena plan to stay behind. Trouble arises during an attempt to close the portal. The four of them are sucked through the door moments before it shuts and disappears. They aren't in Storybrooke anymore.
The heroes come across a skittish groundskeeper who claims he'll be punished if he helps them with magic. ZAP! The heroes are knocked unconscious by a second man. They wake up in a cell. Their captor, the Warden, believes the heroes were sent there by the Dark One. The gardener from before sneaks in to say he will help the heroes if they promise to take him back to Storybrooke. He'll need Zelena's wand.
The gardener sneaks into an asylum laboratory where he restores Zelena's wand. The man who zapped the heroes discovers him there. A scuffle ensues. He forces the gardener to drink a potion. A few harrowing moments later, the gardener transforms into the Warden. They are one in the same. The Warden strikes the other man as a reminder that no one hurts his other self. No one hurts Dr. Jekyll. The Warden has decided to let the doctor go forward with his plan, as he wants to go to Storybrooke, too.
In the backroom of a New York library, Henry finds many storybooks that are similar to his. The stories inside them don't look familiar, but that doesn't mean they aren't real. One of the images looks a lot like the dungeon cell that currently holds several heroes. Violet sees a something that looks like the Holy Grail. It could be the end of all magic. They look to make an escape with the cup, but Mr. Gold arrives before they can. He magically renders them unconscious to reclaim the Olympian Crystal.
Henry lets his moms know that Gold has the Olympian Crystal. He's angry. He still wants to destroy magic. That's why he doesn't reveal that he has the cup in his backpack. Regina and Emma realize that their magic is gone. Gold has all the power. He wants to use it to awaken Belle. Before he can do so, the Warden opens a portal and captures the box that holds her. Now someone else has the power to get the Dark One to do whatever he says.