A huge spaceship called the Ark is headed for Earth. On board are many of the remaining Autobots, answering the call of Optimus Prime. Close behind, Starscream is on-board a Decepticon ship, filled with Decepticons such as Soundwave, among others. As the Ark approaches Earth, the Decepticons damage the ship and it crash lands on the side of a volcanic mountain in a desert region of the United States.

The Decepticons are under the "leadership" of Starscream, returning to Earth to seek revenge. However, Soundwave double crosses Starscream, and finds a way to bring the ship into the Ocean, where Megatron awaits. It is there, under the water, that the Decepticons build a base of operations.

Sam and Mikaela start out the movie having married between films. That takes care of any possibility of a Will Turner/Elizabeth Swann type love story, plus it takes out the "will they/won't they" and leaves room for more of what we're all there to see anyway: TRANSFORMERS.

Meanwhile, Optimus leads the Autobots to the crash site of the downed Ark where they form a headquarters.

In the desert lives a boy that already feels like he's been outcast from society. People look at him differently. Living in the desert, he's become great with computers, and wishes he could live a "normal" life. His name is Chip Chase, a young computer genius that is confined to a wheelchair. When one of the Autobots is in trouble near by, he is able to come to their aide, and eventually comes to help them out at their base. No longer the outcast, he is one of many that people now admire, the perfect teammate for the Autobots. (In the original animated series, Prowl's "battle computer" is damaged in a fight with Decepticons. He then goes online to seek help from the Autobots or from Teletran 1, the computer system in the Ark. He, instead, communicates with Chip, who gives him a hand.)

Without the All-Spark Cube, the Decepticons have a new goal: Energon. They'll take it from wherever they can. And the Autobots have to stop them from getting too much of it, or they'll be able to construct a new All-Spark Cube.