Cyrus distracts the Caterpillar while Alice swipes the compass he gave him awhile back. A Tweedle reveals that the Red Queen was forced to make all of her wishes. Jafar now has control of all three bottles and the Jabberwocky on his side. He also has the Red Queen. Alice and Cyrus use secret tunnels to make their way into Jafar's palace. The Red Queen says if they can save the Knave they can save Wonderland.
In the past, Anastasia (who would become the Red Queen) meets the current queen, Cora. A discussion of magic arises. Cora offers to teach it to Anastasia. That offer is politely declined. Cora overhears Anastasia having a chat with Will (aka the future Knave) about their past. She approaches Will to say his true love has a new life now. Anastasia doesn't need him as a distraction now.
Will is crushed. He asks Cora to take away his heart. He won't be able to love again. Will had no idea that Anastasia was heading out to meet up with him. Cora had a talk with her before she could leave. She played upon her issues with her mother to convince her that she should stay so that she can lead the life she was meant for—the life of a queen. Cora promises to teach her everything she needs to know. This includes magic.
Jafar employs magic on the genie bottles he has in his possession, but he fears he's doing something wrong. Actually, the genie is resisting his spell. The Jabberwocky offers to help. She wants to get inside the Knave's head, but she can't read him. The Red Queen put some kind of protection spell on him. It's her they need to work on. The Jabberwocky realizes the reason they can't get to the Knave is because he doesn't have a heart. She also knows there are intruders about.
Alice and Cyrus realize they need to get the Knave's heart. That'll be a challenge because it's not in Wonderland. They have the White Rabbit take them to Storybrooke. That's where he found the Knave in the first place. The group heads to his apartment. They find the Knave's heart hidden inside a wall. They return to Wonderland where the compass finds something. It's Jafar. He wants the heart. The Knave told him where it was to save the Red Queen.
Jafar tries to destroy Alice and Cyrus, but he's unable to do so. It's his staff. It's not working for him. Cyrus gets control of it, but Jafar runs off with the Knave's heart. The compass points to the staff. Cyrus knows his mother was always fascinated with serpents. This would explain how the staff fought against Jafar. If Cyrus's mother is inside the staff, they need to free her. But how?
Jafar returns to his dungeon as the Red Queen is asking if the Knave he will ever be able to forgive her. It could happen. Anything is possible in Wonderland. Jafar pops the Knave's heart back into his chest. The Red Queen yells for her true love to look at her. He does. All of the feelings these two once had for each other come rushing back.
The Red Queen and the Knave of Hearts share a passionate kiss. Actually, this kiss belongs to Will and Anastasia. Yes, anything is possible in Wonderland. This magical moment ends when Jafar pulls the Red Queen from her cell. He forces an anguished Knave to watch helplessly as he stabs his true love with a dagger.