In Jasper, Nevada, three young humans - Jack Darby, Miko Nakadai and Rafael Esquivel - are accidentally caught in the crossfire in a fight between giant, mechanical aliens that transform into ordinary vehicles.

The Decepticon leader Megatron returns from a three-year exile with a plan to exploit the properties of a mysterious substance called "Dark Energon", which has the ability to turn the bodies of dead Transformers into zombies.

Optimus Prime and Ratchet head out to investigate Megatron's activities while Arcee and Bumblebee go on patrol, leaving Bulkhead with Jack, Miko and Rafael at the base.

Bulkhead, Arcee and Bumblebee sneak on to the Decepticon warship, the Nemesis, to rescue Agent Fowler, while Optimus Prime and Ratchet fight off Megatron and a horde of Dark Energon zombies.

With the Decepticons completing their Space Bridge to Cybertron, Optimus Prime and the Autobots race to stop Megatron from opening the Bridge and bringing forth a vast army of Dark Energon zombies from the Transformers' dead home planet.

Following Megatron's supposed death, Starscream appoints himself as the new Decepticon leader.

While on a scouting mission in the Arctic, Bulkhead and Bumblebee find a crashed space pod buried in the ice.

The Autobots receive a message from Wheeljack, an old friend of Bulkhead's from the days of the war, who is visiting Earth while journeying across the galaxy.

Agent Fowler asks for the Autobots' assistance in transporting a powerful nuclear device to a military base, but since sending such a device through the Ground Bridge could be potentially dangerous, they have to travel by road.

The Autobots discover that an Energon Harvester, an ancient and powerful device from Cybertron's distant past, is on display in a museum, and they attempt to retrieve it with Jack, Miko and Rafael's aid before it falls into the wrong hands.

In an attempt to get even with school bully Vince, as well as impress his crush Sierra, Jack convinces Bumblebee to help him win an illegal street race.

Jack accompanies Arcee on a routine scouting mission in a forest, where they discover a crashed space ship in a clearing.

While exploring the wreckage of a crashed Autobot spaceship in a desert, Optimus Prime becomes infected with Cybonic Plague, a deadly virus that leaves him in a critical condition.

Megatron's subconscious is mistakenly downloaded into Bumblebee's head.

Starscream attempts to use a shard of Dark Energon to revive the dead body of Skyquake, but his plan is impeded by the Autobots.

During a fight with Bulkhead in an abandoned town, Breakdown is captured by M.E.C.H., who wish to dismantle him and research his inner workings for a project they refer to as "Project: Chimera".

Airachnid teams up with M.E.C.H. in a plot to kidnap Jack's mother, June, intending to use her as bait to lure Jack and Arcee to M.E.C.H.'s hideout, so Arcee can be captured and used in M.E.C.H.'s experiments.

Bulkhead and Arcee, with Miko tagging along, are sent on a reconnaissance mission to investigate a bizarre energy signal.

Bulkhead, Arcee, Jack and Miko investigate an old Decepticon Energon mine that was supposedly stripped clean.

Megatron sends Starscream and Airachnid to the site of a crashed Decepticon ship to recover The Immobilizer, a powerful weapon with the ability to freeze Transformers in their tracks.

Miko rushes out onto the battlefield during a fight between the Autobots and the Decepticons, who are fighting over a Data Cylinder, a device containing knowledge of Cybertronian society.

Ratchet tests the Synthetic Energon formula obtained by Bulkhead on the Data Cylinder on engines.

Optimus Prime recites a passage from the Covenant of Primus, detailing a doomsday prophecy connected to Earth and involving Megatron.

Unicron the Chaos-Bringer, an ancient and malevolent being, awakens from the center of the Earth after millennia of stasis, causing an epidemic of natural disasters across the globe, and sending Dark Energon erupting from volcanoes.