In 1851, nine years after the events of the first film, Don Alejandro de la Vega is married to Elena and has a son, Joaquin. California is voting on whether to join the United States of America as a state. Zorro foils a plot to steal ballots. During the fight with a gunman named Jacob McGivens, he briefly loses his mask. A pair of Pinkerton agents sees his face and recognize him. The following day, the Pinkertons confronts Elena and force her to divorce Alejandro.
Three months later, Alejandro is living in a hotel. The separation from Elena and the feeling that the people no longer need Zorro are taking its toll on him. His childhood guardian, Father Felipe, convinces him to attend a party at French Count Armand’s new vineyard. There, Alejandro discovers that Elena is dating the count. After leaving the party, Alejandro witnesses a huge explosion close to Armand’s mansion and becomes suspicious of him.
McGivens leads an attack on the family of Guillermo Cortez, Alejandro’s friend, to seize their land deed. Donning his mask again, Zorro rescues Guillermo’s wife and son, but fails to save Guillermo and the deed. Zorro follows McGivens to at Armand’s mansion and discovers that Armand plans to build a railroad on Cortez’s land. Zorro encounters Elena, and learns of an upcoming shipment. He tracks McGivens to a cove where the cargo is delivered. Unbeknownst to him, Joaquin also hitched a ride on McGiven’s cart, having sneaked out of a class trip. Zorro saves his son from the bandits. Examing the shipment, he sees a piece of the cargo, a bar of soap, and the name Orbis Unum from a crate lid.
Felipe and Alejandro then learn that Armand is the head of a secret society, the Knights of Aragon, which has been secretly ruling Europe. The United States is deemed a threat to the Knights. Thus, they plans to throw the country into chaos before it can gain too much power. Alejandro is then captured by the Pinkertons. They reveal to him that they forced Elena to divorce Alejandro and get close to Armand and learn of his plans.