The Autobots continue to work for NEST, now no longer in secret. But after discovering a strange artifact during a mission in Chernobyl, it becomes apparent to Optimus Prime that the United States government has been less than forthright with them.

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.