Two years after their battle in Mission City, the Autobots have joined forces with a secret military organization called NEST to track down any remaining Decepticons on Earth. Meanwhile, Sam Witwicky, now preparing to leave for college, discovers a fragment of the AllSpark—a powerful artifact that both Autobots and Decepticons seek—has imprinted knowledge of ancient Cybertronian symbols into his mind. Unwittingly, Sam becomes a target for the Decepticons, who believe he holds the key to finding a new energy source.

As Sam heads off to college, trying to maintain a normal life and leave the past behind, he is relentlessly pursued by the Decepticons, who need the information locked inside his brain. The pursuit escalates quickly, thrusting Sam, his girlfriend Mikaela, and his robot ally Bumblebee into a global conflict. With the Decepticons gathering strength and a menacing entity known as The Fallen preparing to rise, the stakes are high for the Autobots to crack the symbols' secrets to protect Sam and prevent a catastrophe that could end life on Earth.