Through flashback we see Alice get hurt in a sword fight. Cyrus brings her to the White Rabbit who saves her. Cyrus acquire magic from he caterpillar to make he and Alice a safe place in Wonderland that no one else can see.
In the present. Jafar tries to steal the genie bottle from the Red Queen but finds it's a fake. He sends a dark cloud to kill her.
The White Rabbit tells Alice that the Queen has taken his family and he's been forced to work for her. The Knave finds them in his and Anastasia's old wagon and releases them.
The Red Queen finds Cyrus. She brings him to Alice, the Knave, and the White Rabbit and wants the White Rabbit to dig a hole out of Wonderland for them all before Jafar kills them.
The Queen says she wants to be with Will and will give up anything to make that happen. Will refuses to believe her. One of Jafar's lightening bolts hits him and he and Alice lay dying because of the first wish she made…that if the Knave dies so will she.
Will gets Alice's last wish per her agreement that she'd give him one if he helped her find Cyrus. Will wishes to end Alice's suffering. Alice wakes up and is happy to be in Cyrus' arms who appears to no longer be a genie, but Will has disappeared. He's in the genie bottle.