Sam Witwicky leaves the Autobots behind for a normal life. But when his mind is filled with cryptic symbols, the Decepticons target him and he is dragged back into the Transformers' war.

Set during the Cold War, the Soviets—led by sword-wielding Irina Spalko—are in search of a crystal skull which has supernatural powers related to a mystical Lost City of Gold. Indy is coerced to head to Peru at the behest of a young man whose friend—and Indy's colleague—Professor Oxley has been captured for his knowledge of the skull's whereabouts.

When an Egyptian terrorism suspect "disappears" on a flight from Africa to Washington DC, his American wife and a CIA analyst find themselves caught up in a struggle to secure his release from a secret detention facility somewhere outside the US.