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 three kids are taken to the base of the Autobots, where the Autobot leader Optimus Prime explains that he and his team are a race of autonomous robotic organisms from the far-off planet Cybertron, and they are fighting over their life-source, Energon, with the Decepticons, with whom they once had a war.
With Cliff Jumper missing, the Autobots go full force to find him. Meanwhile, Megatron grows stronger as he obtains more and more Dark Energon.
When Agent Fowler is kidnapped by Starscream and the Decepticons, Bulkhead goes on a rescue mission with Miko by his side.
Optimus Prime and Ratchet struggle to take on Megatron's newly resurrected Terrorcons while Bulkhead, Arcee and Bumblebee battle the Decepticons in order to rescue Agent Fowler, who's imprisoned on the Nemesis.
Megatron sets his sights on resurrecting the fallen Cybertronians with the use of his Dark Energon. Now Optimus Prime and the rest of the Autobots must fight back and protect the planet from destruction.
While Starscream searches for the legendary Decepticon Skyquake, Optimus Prime and Bumblebee head out to monitor a disturbance in Energon readings. Meanwhile, Ratchet, Arcee and Bulkhead help the humans with their science projects.
With Optimus Prime and Arcee currently away in the Arctic, Bumblebee, Bulkhead and Ratchet must work together with the humans to save headquarters from the evil Scraplets.
Bulkhead is elated to learn that his good friend and former war hero Wheeljack is headed towards Earth. Meanwhile, Starscream and Makeshift plan to hijack Wheeljack's arrival in an attempt to learn the location of the Autobot base.
Agent Fowler enlists the Autobots' help in transporting a prototype energy source that could be disastrous in the hands of the Decepticons. Unfortunately, the Autobots have more than Decepticons to worry about when they are targeted by a human organization known as M.E.C.H. and their formidable leader Silas.
When the Autobots receive word of an Energon Harvester in Greece, Bulkhead takes Miko with him to hunt it down. Upon arrival, a Decepticon named Breakdown attacks Bulkhead and Miko. Meanwhile, Starscream and Soundwave call upon Knock Out to help revive Megatron. Later, the Autobots discover the Energon Harvester's location and must break into a museum to obtain it before the Decepticons.
While trying to impress Sierra, Jack becomes involved in an illegal street racing circuit. Unfortunately, Jack discovers that the Decepticon Knock Out is also participating in the race. During the race, Knock Out mistakenly abducts Jack's schoolmate, Vince. The Autobots must now rescue Vince while dealing with a simultaneous attack from Breakdown.
While on a routine patrol in the forest, Jack and Arcee find a crashed spaceship which belongs to the latter's archenemy Airachnid, who strikes a lot of fear in Arcee as a result of a previous encounter. Airachnid's presence on Earth makes her a threat to the human race and Jack will be her first target unless Arcee overcomes her fears and battles the evil spiderbot.
With Optimus accidentally infected by the deadly Cybonic plague virus, Arcee and Bumblebee must sneak into the Decepticon base to recover an antidote. Once inside, they learn of Megatron's comatose state and come up with a plan to retrieve this antidote by accessing Megatron's mind. Meanwhile, Starscream and Knockout devise a plan to put Megatron offline permanently. But with Bumblebee stuck inside Megatron's mind, his life and the life of Optimus are both at stake.
The team starts to notice Bumblebee's odd behavior and wonders what the problem might be. Upon further inspection, they learn that his brain is being controlled by Megatron.
Starscream begins plotting his revenge against the newly revived Megatron by stealing a Dark Energon crystal with which he plans to resurrect Skyquake. But when Miko and the others follow the Autobots to Starscream's coordinates, the two competing GroundBridges malfunction and accidentally send the kids to an alternate astral plane where they can't be seen or heard by the Autobots. Unfortunately, Skyquake is also stuck in the Shadowzone with Miko, Raf and Jack, putting their lives in danger.
During a battle between Bulkhead and Breakdown, Breakdown is captured by Silas and his MECH agents so they can dissect him to better understand Cybertronian technology. Figuring Megatron won't mount a rescue for a fellow Decepticon, Optimus Prime assembles his team to do so, much to Bulkhead's shock. Initially, he refuses to help his archenemy, but Miko convinces him to go so he can get a long awaited rematch against him. Bulkhead is first to find Breakdown and the two must work together to escape from MECH.
Airachnid makes a deal with Silas to get revenge against Arcee and Jack.
The Autobots and Decepticons race to claim a magnetic weapon. In the ensuing battle, the Bots are forced to fight while stuck together!
While searching for traces of Energon in a cave, Arcee, Bulkhead, Jack and Miko get unexpected company when Megatron and Starscream arrive as well. The ensuing battle between Autobots and Decepticons causes a cave-in, leaving them trapped inside struggling to survive and find a way out.
Starscream makes an unexpected request after he is captured by Optimus.
The Decepticons hunt Bulkhead down when he gains possession of the secret formula for synthetic Energon. Unfortunately, the data inside his head is slowly erasing portions of his brain. Unless the Autobots can come up with a solution, Bulkhead will never be the same.
Ratchet's devotion to the Autobots is tested when he believes that he has perfected the formula for synthetic Energon. But when Ratchet uses himself as the test subject, the synthetic Energon begins to alter his personality.
When the Autobots learn of the Decepticons' plans to build a Space Bridge, Optimus decides to face Megatron once and for all.
The Autobots discover that Dark Energon is responsible for Earth's recent natural disasters.
The Autobots team up with a surprising ally to save Earth.
While the Autobots continue their battle at the Earth's core, Jack learns more about Optimus' history on Cybertron.