Plot
Some time after defying the Wonderful Wizard of Oz, Elphaba Thropp, now branded as the Wicked Witch of the West by Madame Morrible, continues battling for Animal rights from a forest hideout. Glinda Upland, now the Wizard's spokesperson, is engaged to Fiyero Tigelaar, now Captain of the Gale Force. As Oz celebrates the grand opening of the Yellow Brick Road, Fiyero reveals he is attempting to locate Elphaba, though Glinda insists Elphaba does not want to be found.
Elphaba encounters some Animals leaving Oz, including her former caretaker Dulcibear, and encourages them to fight against the Wizard. The Cowardly Lion dissuades them, blaming Elphaba for freeing him from his cage as a cub, the only home he had known, and exposing her as the reason for the Wizard's flying monkey spies. Elphaba visits her sister Nessarose, who has inherited their father's governorship of Munchkinland. Nessarose prohibits the Munchkins, including her servant Boq, from leaving without her approval. Elphaba enchants Nessarose's shoes, giving her the ability to fly. Boq, deciding Nessarose no longer needs him because of this and having learned of Glinda and Fiyero's wedding, tries to leave Nessarose. She casts a love spell from the Grimmerie, but it backfires, shrinking his heart. Elphaba's attempt to save him turns him into a tin man.
Elphaba returns to the Emerald City, where Glinda implores her to join the Wizard. She accepts under the condition that the flying monkeys be freed. Chistery, one of the monkeys, reveals several Animals imprisoned within the Wizard's lair, including Dr. Dillamond, who has lost his ability to speak. Reaffirming her resolve to fight the Wizard, Elphaba frees the Animals, interrupting Fiyero and Glinda's wedding. Fiyero helps Elphaba escape and joins her. Concluding that they are having an affair, Glinda vengefully suggests that the Wizard and Morrible lure out Elphaba by spreading a rumor that Nessarose is in trouble.
At their hideout, Elphaba and Fiyero profess mutual love. He suggests that she should go to an abandoned castle, Kiamo Ko, for shelter. Morrible, realizing a simple rumor would not fool Elphaba, creates a tornado that brings a house from Kansas that fatally crushes Nessarose. Glinda gives Nessarose's shoes to the house's occupant, Dorothy Gale, and directs her to the Wizard, promising that he can help her return home. A fight begins between Glinda and Elphaba before the Gale Force arrives. Fiyero intervenes and holds back the guards by threatening to kill Glinda, and he finally accepts that he loves Elphaba. While the guards drag Fiyero into a field and savagely beat him as punishment, Elphaba escapes with the monkeys to Kiamo Ko, where she casts a spell to save Fiyero's life. Believing she has failed, and lamenting all her previous failed attempts to do right, she decides to embrace her perceived "wickedness".
Dorothy, alongside Boq, the Lion, and a scarecrow, meets the Wizard, who instructs them to kill Elphaba and bring him her broom. Boq rallies the citizens of the Emerald City against Elphaba. Lamenting that her public image is built on lies, Glinda confronts Morrible about the tornado, but Morrible rebuffs her. Glinda rushes to Kiamo Ko to warn Elphaba about the mob. Elphaba kidnaps Dorothy and imprisons her to retrieve the shoes just as Glinda arrives. After Chistery informs them of Fiyero's apparent death, Elphaba decides to surrender, imploring Glinda to withhold the truth from the people and entrusting her with the Grimmerie. They reaffirm their friendship in a tearful farewell. Glinda hides and watches in horror as Dorothy douses Elphaba with a bucket of water, seemingly melting her.
Having regained speech, Chistery gives Glinda the green elixir bottle that belonged to Elphaba's mother. She brings it to the Wizard, who realizes that he is Elphaba's biological father and the reason for her power. Ashamed of his actions, he leaves Oz at Glinda's demand. Glinda directs the monkeys to apprehend and arrest Morrible for her crimes. She finishes telling her story to the Munchkins and reestablishes rights for the Animals, who get their voices back. The Scarecrow – revealed to be Fiyero, transformed by Elphaba's spell – returns to Kiamo Ko and finds Elphaba hiding under a trapdoor, having faked her death to protect Glinda's reputation. Elphaba and Fiyero depart Oz through the surrounding desert while the Grimmerie opens for Glinda.
