In Transformers: Revenge of the Fallen, two years have passed since Sam Witwicky (Shia LaBeouf) and the Autobots saved the human race from the invading Decepticons. Now he's preparing for the biggest challenge of his life: leaving home for college. Despite his extreme heroics, the battle of Mission City has become an urban legend believed only by conspiracy theorists. Sam is still an average teenager with everyday anxieties and excitement about heading off into adulthood, separating from his parents (Kevin Dunn and Julie White) for the first time, and vowing to be faithful to girlfriend Mikaela (Megan Fox). Of course, he also has to explain his departure to his guardian robot, Bumblebee.
Leaving home is something the Autobots understand only too well. With the destruction of the Allspark, the Transformers home planet of Cybertron is uninhabitable, and the Autobots make the best of their lives on earth, working in league with the military as part of a TOP SECRET team called NEST. Operating alongside their human counterparts, field commanders Major Lennox (Josh Duhamel) and USAF Master Sergeant Epps (Tyrese Gibson), the NEST TEAM seeks to hunt down whatever remaining Decepticons are still hiding on earth.
Unfortunately, even as the Autobots try to make a new life among humans, they discover they may not be welcome.
National Security Advisor Theodore Galloway (John Benjamin Hickey), driven to prove that all Transformers should be banished from earth, endeavors to terminate NEST, believing the Autobots' very presence may endanger the human race. Optimus Prime, the leader of the Autobots, agrees to leave our planet if the governments of the world wish it... but he warns Galloway to consider what happens if the Autobots leave earth defenseless.
Meanwhile at school, Sam adjusts to his pushy, legend-in-his-own mind roommate, Leo (Ramon Rodriguez), and an equally aggressive temptation in the form of a new co-ed, Alice (Isabel Lucas). Sam does his best to navigate college life, until suddenly he's besieged by visions flashing across his brain like thunderbolts. The Decepticons soon learn what Sam doesn't know; that he alone holds the key to the outcome of the struggle between evil and the ultimate power of good.
A normal life will have to wait. With the help of the Autobots, the soldiers of NEST, and an old adversary-turned-ally (John Turturro, returning as former Sector 7 Agent Simmons), Sam and Mikaela must uncover the secret history of the Transformers presence on earth, and the sacrifices that have to be made to save it from an ancient threat sworn on returning here for revenge... an ancient Decepticon named THE FALLEN.