In 1961, a Cybertronian spacecraft lands on the dark side of the moon. Known as The Ark, it was the last ship to escape a Cybertron devastated by wars. Piloted by Sentinel Prime, it carried "the Pillars", technology that could save the Cybertronians once and for all. On earth, the crash of The Ark is detected by NASA, and President John F. Kennedy authorises the mission to put a man on the moon. In 1969, Apollo 11 lands on the surface of the moon to collect samples from The Ark.
In the present day, the Autobots have forged a military alliance with the United States of America, but largely act independently in stopping humans from destroying themselves. During a mission in Chernobyl at the request of the Ukrianian government, Optimus Prime discovers a fuel cell from The Ark that the Soviet Union attempted to use as a power source, resulting in the Chernobyl disaster. Optimus is devastated at the news that humans lied to the Autobots - knowing as he does the contents of the ship - and launches his own mission to retrieve the Pillars and revive Sentinel Prime. Just five Pillars remain on-board The Ark, which the Autobots as describe as being the means to establish a mobile space bridge between two points and transport matter through. Charlotte Mearing, the Secretary of Defence is hurried at this revelation as the Pillars could be used to bring an invading army to earth.
Meanwhile, Sam Witwicky is frustrated by his life after graduating from college as he is unable to find a job. He takes his frustrations out on his girlfriend, Carly Spencer, and her close relationship with her playboy accountant boss, Dylan Gould. Sam eventually finds employment in a mail room in a high pressure working environment. One of his co-workers, Jerry Wang, takes an unusual interest in Sam's activities before revealing himself to be a conspiracy theorist. He passes information on to Sam about "the dark side of the moon" before being assassinated by Laserbeak, a condor-like Decepticon. After contacting the retired Seymour Simmons, Sam realises that the Decepticons are systematically targeting people connected to the American and Russian space missions. They are able to locate one of a handful of Russian cosmonauts who fled to America after the Soviet space program was shut down. The cosmonauts are in possession of photos taken by Soviet satellites that clearly show hundreds of Pillars being stockpiled. Sam realises that the Decepticons raided The Ark decades beforehand and are luring the Autobots into a trap: unable to revive Sentinel Prime on their own, they left him and five Pillars - including the Master Pillar, which controls all of them - for the Autobots to find. Sam manages to contact the Autobots and reveal that Sentinel Prime is being targeted by the Decepticons, and they manage to escort him to their base. Sentinel then reveals that he has made a deal with the Decepticons and betrays both the Autobots and the humans, destroying their base and executing Ironhide before fleeing with the Pillars.
Sentinel uses the Pillars to establish a space bridge with the moon, where hundreds of Decepticons have lain in wait for decades. Sam is forced by Dylan Gould - revealed to be the Decepticons' agent on earth - into finding out Optimus Prime's plans for retaliation. He manages to warn Optimus not to say anything as "no human will ever know". The Autobots are exiled from earth by way of a decommissioned Cybertronian spacecraft salvaged from the original landings. However, the Decepticons are lying in wait and shoot the rocket down before taking control of earth. With Gould's help, they establish themselves in Chicago and fortify the city. Gould reveals to a kidnapped Carly that the Decepticons intend to rebuild Cybertron, strip-mining the earth for resources and using humans as slave labour. In order to do this, the Decepticons have placed Pillars around the world to call Cybertron itself through the space bridge.
Angered at the betrayal, Sam finds USAF Chief Robert Epps and the two re-form Epps' disbanded NEST team to go into Chicago and rescue Carly. They are very nearly killed before they have set foot in the city and are saved by the return of Optimus Prime and the Autobots, who escaped the explosion of their shuttle by hiding in one of the booster rockets that was disengaged before the Decepticon attack. Sam, the Autobots and NEST advance on Gould's penthouse to rescue Carly and disable the Master Pillar before Cybertron appears in the sky. After battling through the city, NEST take out the Decepticon leaders while Carly convinces Megatron that he will answer to Sentinel Prime once Cybertron is restored, instead of leading the Cybertronians himself. Sam is able to get to the Master Pillar where he confronts Gould. Gould is electrocuted by the Pillar, which Bumblebee smashes to pieces. The connection to Cybertron is broken, and the half-formed planet collapses in upon itself. With Cybertron destroyed, Optimus and Sentinel fight one another in the ruins of Chicago. Optimus loses an arm and is about to be killed by Sentinel before Megatron intervenes, having believed Carly. This gives Optimus the opening he needs to re-enter the fight, ripping Megatron's head and spine from his body before executing Sentinel. Sam and Carly are reunited while the Autobots accept that with Cybertron gone, Earth is now their only home.
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