In Wonderland
Jafar and Amara successfully break the laws of magic, becoming the two most powerful sorcerers in all the realms. However, despite this, Jafar refuses to share the title with Amara and tries to kill her as Amara attempts to heal Cyrus. Jafar is interrupted by his father, who wants nothing but the madness to end. Wanting to get the love he never got from his father, Jafar uses his magic on his father to love him and then coldly kills him. Amara and Alice use this commotion to flee the castle with Cyrus on a magic carpet. They seek refuge at the White Rabbit's home, where Amara heals Cyrus. Alice hatches a plan with Cyrus, Amara, and the White Rabbit to defeat Jafar and they part ways in two teams; Alice and the White Rabbit to find people to help fight Jafar, while Amara and Cyrus head to the Well of Wonders to return the magical waters to Nyx to undo Jafar's spell. Jafar raises the dead and commands them to hunt down and kill Alice, Cyrus, and Amara. He also resurrects Anastasia, who is under the impression that she is Jafar's lover.
Alice and the White Rabbit, after gathering some men and women, fight against Jafar's undead army, and Alice is promptly captured and taken to the castle. Jafar interrogates Alice to learn Amara's whereabouts and learns about their plan involving Nyx and the Well of Wonders. With Anastasia's help, Jafar heads over to eliminate Amara. Upon reaching the doorway to the Well of Wonders, Amara and Cyrus are ambushed by the undead army. Using her magic, Amara kills them and proceeds to sacrifice herself to Nyx as Jafar confronts them. In the mid of this, Alice and the White Rabbit ambush Jafar. As Amara slowly condensers into water, Jafar steals the water before it could be fully returned to Nyx. Believing that he defeated Alice and Cyrus, Nyx, angered that he stole her waters without her permission, curses Jafar into a genie and his genie bottle is sent to another realm. Once Jafar is defeated, his wrongdoings are undone; Will, Taj, and Rafi are freed from their genie imprisonment, and Anastasia remains dead. However, Nyx believes that, while the Red Queen was meant to move on, Anastasia's path lives on and instead she gifts Alice and Cyrus her waters to awake Anastasia. Will, upon Anastasia dying again, grieves her death again. When Alice and Cyrus return to the castle, they give Nyx's waters to Anastasia which awakens her. She reunites with Will as Cyrus reunites with his brothers. With nothing left to lose, Alice suggests that they return to Victorian England for their marriage. With the White Rabbit's help, Alice and Cyrus return home.
In Victorian England
Sometime after returning home, Alice prepares to wed Cyrus. On her wedding day, her father Edwin apologies for never believing in her tales of Wonderland. He walks her down the aisle while their guests: Sarah, Millie, Anastasia, Will, Taj, Rafi, Mrs. Rabbit, and Tweedledum look on. After reaching the end of the aisle, as Alice and Cyrus stand together, the White Rabbit officiates the wedding by talking about how Alice and Cyrus have stayed by each other through thick and thin and officially pronounce them as husband and wife. After the ceremony, Alice and Cyrus bid farewell to their friends as the White Rabbit sends everyone back home via his portal.
Many years later, while having tea with Cyrus in the garden of their home, Alice tells her tales of Wonderland to her daughter, noting that Anastasia and Will have become the White Queen and King of Wonderland while the White Rabbit looks in on the happy family.