In 1967, British spy Austin Powers attempts to assassinate his nemesis, Dr. Evil, in his own nightclub. Dr. Evil escapes, freezing himself. Thirty years later, Dr. Evil returns with plans for world domination. Austin Powers, along with agent Vanessa Kensington, is unfrozen to stop him. They pose as a married couple and infiltrate Dr. Evil's headquarters, encountering fem-bots and other obstacles. Ultimately, Powers deactivates Dr. Evil's doomsday device and defeats him, marrying Vanessa. However, they are attacked by Random Task, indicating that Dr. Evil is still a threat.

Dr. Evil has invented a time machine to go back to the 1960s and steal Austin Powers' mojo, leaving him shagless. With the help of Felicity Shagwell, Austin travels back in time to stop Dr. Evil and save the world.

Austin Powers learns that his father has been kidnapped, so he travels back in time to 1975 to rescue him and stop the villain Goldmember from causing global flooding. With the help of his old flame Foxxy Cleopatra, Austin infiltrates Goldmember's roller disco club, confronts Fat Bastard in Tokyo, and teams up with his long-lost brother Dr. Evil to save the world. In the end, they defeat Goldmember and reconcile as a family.