With Amara's reluctant assistance, Jafar is able to turn them both into the most powerful sorcerers in the world. The old man, the former sultan, tells his angry son that the way to show true power is with mercy. Jafar uses his new power to make his father express his pride and love for him. Then he murders him. Jafar turns his attention to Amara, Alice and the critically-wounded Cyrus, but they are gone. They've managed to escape via a magic carpet ride as Jafar proceeds to kill the Jabberwocky.
At the White Rabbit's house, Amara uses her powers to save Cyrus. Alice is overjoyed, but there no time to celebrate. They need to act as a united front to take down Jafar, who has brought the Red Queen back to life. Will is elated until he discovers the catch. Jafar brought Anastasia back so the she could be with him. He summons others who are dead to rise up from the grave. He orders his undead army to hunt down Amara and kill anyone in their way. Jafar wants them to bring Wonderland to its knees.
The stolen water needs to be returned to Well of Wonders in order for Jafar to lose his magic. Cyrus and Amara encounter Jafar's army on their way there. Elsewhere, Alice recruits soldiers to storm Jafar's castle. She gives a stirring speech that inspires the ragtag group. They also encounter Jafar's troops. Amara is able to overcome the soldiers with her powers. Alice, however, is unable to fend off the massive army. She's captured. Jafar wants her to help him find Amara. He threatens to change her past. She'll go back to being a lonely little girl in England who never met Cyrus. It'll be as if she never loved at all.
Alice refuses to help Jafar. The true love she shares with Cyrus is more powerful than his magic. It can never be destroyed. Jafar turns his attention to the Red Queen. She warns that Amara and Cyrus are headed to the Well of Wonders. Jafar is off to find them. The Knave tries to talk the Red Queen into helping them, but only one thing can snap her out of her curse: true love's kiss. Will and Anastasia lock lips. The spell is broken. They are off to stop Jafar.
Nyx, the guardian of the Well of Wonders, appears before Amara, who steps forward to complete her journey. FLASH! Amara is knocked to the ground by a streak of lightning from Jafar. She dissolves away into water. Jafar is about to strike Cyrus when Alice bursts up from a portal created by the White Rabbit. It's not enough to stop her foe though. Jafar steals the water that's supposed to go into the well. Alice is undaunted. She tells Jafar that it's not her who is going to defeat him. It's the one from whom he stole the water.
Nyx rises up once again. She tells Jafar that the water does not belong to him. His fate will be to serve the desires of others. Moments later, Jafar is trapped inside a bottle. He's now a genie. Cyrus and Alice are reunited. They share a kiss. Cyrus is also reunited with his brothers. He shares the news that their mother gave her life for them. The Red Queen is also gone, but the guardian of the Well of Wonders believes that Anastasia's path was meant to continue. Cyrus gives Will some water. It wasn't stolen. It was given. A few drops on Anastasia's lips and she is revived. She is reunited with Will to share true loves kiss once again.
Alice is ready to leave Wonderland. Back in England, Alice's father lets his daughter know that he is proud and happy to welcome Cyrus into their family. He walks Alice down the aisle on her wedding day. All of Alice's closest friends are amongst the guests. The White Rabbit performs the ceremony. Vows and rings are exchanged and Cyrus is allowed to kiss the bride. After the wedding, Alice thanks the White Rabbit for bringing her to Wonderland. She bids adieu to Anastasia. She gives her good friend Will a special hug. They advise each other to hold onto their hearts.
Years later, Alice reads a story to her young daughter. It's all about her adventures in Wonderland. The young girl believes all that happened to her mother is impossible. Alice assures her that nothing is impossible in Wonderland. Cyrus appears with a tray in hand. The entire family is going to have a tea party. A certain White Rabbit oversees this happy event from a distance. He shares a special bond with a girl named Alice. They were both part of something magical that took place Once Upon a Time in Wonderland.