Two years after the Autobots destroyed the Allspark and defeated Megatron, a secret organization called NEST works together with Autobots to elimate the Decepticon threat for good. However, the government is not completely convinced that the Autobot's actions are still neccesary and believes that their presence is incurring the Decepticon's wrath. Optimus Prime tries to convince their old ally, Sam Witwicky, to convince the government that the Autobots are needed. But Sam is more concerned about starting college and maintaining his relationship with Mikaela. However, this proves difficult as Sam is constantly seeing alien symbols after being exposed to a remaining piece of the Allspark. When the Decepticons and a recently resurrected Megatron become aware of what Sam knows, they try to extract the information from him. After Optimus Prime is killed trying to defend Sam, he and the Autobots must find out the meaning of the mysterious symbols before it's too late.