When vengeful General Francis X. Hummel seizes control of Alcatraz Island and threatens to launch missiles loaded with deadly chemical weapons into San Francisco, only a young FBI chemical weapons expert and notorious Federal prisoner have the skills to penetrate the impregnable island fortress and take him down.

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.