The film opens on the homeworld of the Maximals, a heroic faction of Transformers who disguise themselves as animals. They are protecting the Transwarp Key, an artifact that can open portals across space and time. Their planet is attacked by Unicron, a massive, planet-eating Transformer, and his herald, Scourge, leader of the vicious Terrorcons.

After their leader sacrifices himself, the Maximals, led by Optimus Primal (a gorilla), flee through a portal to Earth with the Key, splitting it into two halves and entrusting one half to a hidden human tribe in Peru for safe keeping.

The story shifts to 1994, Brooklyn, New York. Noah Diaz, an ex-military electronics expert, is struggling to find work to pay for his younger brother Kris's medical care. Desperate, he attempts to steal a Porsche, which is revealed to be the wisecracking Autobot, Mirage.

Concurrently, museum researcher Elena Wallace is studying an ancient falcon statue. She accidentally breaks it open, revealing one half of the Transwarp Key hidden inside. The key releases an energy pulse that is detected by both the stranded Autobots (led by Optimus Prime) and the villainous Terrorcons.

The Terrorcons, led by Scourge, arrive on Earth and attack the Autobots to seize the artifact. In the ensuing fight, the Autobot Bumblebee is gravely wounded and seemingly killed by Scourge, who steals the half of the Key. The battle is interrupted by the Maximal Airazor (a peregrine falcon), who repels the Terrorcons and informs the Autobots that the key was split into two.

Optimus Prime, desperate to use the Key to return the Autobots home to Cybertron, reluctantly teams up with Noah, Elena, and the remaining Autobots. Elena deduces that the other half is located in a hidden temple in Peru, leading the group to travel there.

In Peru, the Autobots and humans rendezvous with the other Maximals, including Optimus Primal. However, the Terrorcons track them down and launch a major attack. During the chaos, Scourge corrupts Airazor with Dark Energon, forcing Optimus Primal to tragically kill his friend to protect Elena.

Scourge ultimately secures the second half of the Key. He reassembles the artifact and uses it to open a massive portal above the Earth's atmosphere, through which Unicron begins to emerge, initiating the consumption of the planet.

The Autobots and Maximals launch a final, desperate assault to destroy the Key before Unicron can fully materialize. Noah and Elena sneak toward the Transwarp Key's control terminal with an access code. During the final battle, Mirage is heavily damaged protecting Noah, but transforms his body into a powered exo-suit for Noah, allowing them to fight together.

As the battle rages, the Energon in the valley re-activates Bumblebee, who returns to the fight and helps turn the tide. Elena reaches the terminal and inputs the code to deactivate the Key, but Scourge, with his last strength, destroys the terminal. Optimus Prime makes the sacrifice, destroying the Key with his sword, collapsing the portal and stranding Unicron.

Optimus Prime is nearly sucked into the imploding vortex but is saved by Noah and Optimus Primal. In the aftermath, the Autobots and Maximals declare Earth their new home and allies. Noah, hailed as a hero, later attends a job interview which is revealed to be a recruitment meeting for the secret military organization G.I. Joe.