In 1961, a Cybertronian spacecraft carrying a lost Autobot leader and a powerful device crashed on the dark side of the Moon. The event was detected by NASA, prompting President John F. Kennedy to authorize the Apollo missions as a cover for investigating the wreckage. Decades later, the Autobots, led by Optimus Prime, continue to assist humanity while secretly hoping to end their war with the Decepticons. During a mission in Chernobyl, Optimus discovers a fuel cell from the lost ship, the Ark, learning it survived its journey from Cybertron. Following this lead, the Autobots travel to the Moon and find their comatose former leader, Sentinel Prime, along with five of his inventions: Pillars capable of creating a Space Bridge to teleport matter across vast distances.

Sam Witwicky, now a young adult struggling to find a job and frustrated by being sidelined from Autobot operations, becomes entangled in the conspiracy. With a new girlfriend, Carly Spencer, Sam uncovers that the Decepticons are systematically eliminating anyone connected to the Apollo program. Teaming up with the eccentric former agent Seymour Simmons, Sam learns the Decepticons had already raided the Ark years before the Autobots and intentionally left Sentinel and five Pillars as bait. The Decepticons lacked the means to revive Sentinel, and they manipulated the Autobots into doing it for them.

Once revived, Sentinel Prime, voiced by Leonard Nimoy, immediately betrays the Autobots, revealing a pact with Megatron to ensure the survival of the Cybertronian race at Earth's expense. He kills the Autobot Ironhide and activates his Pillars, teleporting hundreds of hidden Decepticons from the Moon to Earth. The Decepticons demand the Autobots be exiled from the planet to avoid a war. As their ship departs, it is shot down, seemingly destroying them. With the Autobots gone, the Decepticons, led by Megatron and Sentinel, seize control of Chicago and begin placing Pillars around the world.

Carly is captured by her charming boss, Dylan Gould, who is revealed to be a human collaborator working for the Decepticons. Gould explains the Decepticons plan to transport their homeworld of Cybertron into Earth's orbit, using the human population as slaves to rebuild their society. Sam, aided by the Autobots who had faked their own deaths, and military veterans like Robert Epps, launches a desperate assault on Chicago to rescue Carly and stop the activation of the Space Bridge. A climactic battle ensues, resulting in the deaths of major Decepticon figures such as Starscream and Shockwave. Optimus Prime, after losing his arm in a brutal fight with Sentinel, is offered a truce by a jealous Megatron, who fears being overshadowed. Optimus refuses, killing Megatron before executing the treacherous Sentinel Prime for his crimes against both humanity and the Autobots.