Ratchet tests the Synthetic Energon formula obtained by Bulkhead from the Data Cylinder on various engines. Feeling the desire to take a more active role in the missions, he injects himself with the formula. At first the results are positive, with the formula greatly increasing Ratchet's strength, speed and agility. But before long, the formula starts to have negative effects on his personality.

Bulkhead and Arcee, with Miko tagging along, are sent on a reconnaissance mission to investigate a bizarre energy signal in the desert. They discover that the signal is coming from a Polarity Gauntlet, a weapon that manipulatesmagnetic fields. However, they soon come into conflict with Breakdown and Airachnid, who both want the Gauntlet for themselves. In the end, though, Arcee and Bulkhead are successful while Breakdown returns to Megatron empty handed aside from Airachnid, who rejoins the Decepticons.

M.E.C.H. and Airachnid team up to kidnap Jack's mom, and Arcee has to offer herself as ransom. M.E.C.H. is after the Transformer technology, while the sadistic Airachnid simply wants to kill everyone involved.

M.E.C.H. capture Breakdown to take him apart and implement the gathered knowledge into their secret plans. The Autobots thus have to rescue their own enemy.

Jack, Raf and Miko get trapped in-between dimensions, along with the revived body of the fallen Decepticon Skyquake. The Autobots have to figure out a way to save them. The battered and humiliated Starscream meanwhile tries to follow up on his latest scheme to overthrow Megatron.

Jack accompanies Arcee on a routine scouting mission in a forest, where they discover a crashed space ship. They soon discover that the owner of the ship, the deadly and ruthless Decepticon sadist known as Airachnid, is still prowling the forest in search of a human to hunt, putting Jack in danger and causing Arcee to have visions regarding her last encounter with Airachnid on Cybertron during a mission with her partner; Tailgate

Debuts: Airachnid and Tailgate

Deaths: Tailgate

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. However, things go awry when Knock Out gets involved in the action, kidnapping Vince in the belief that he is Bumblebee's human partner.

Debuts: Vince

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. Starscream also learns of the Harvester's whereabouts, and he sends Soundwave, along with new Decepticons Knock Out and Breakdown, to obtain it.

Debuts: Knock Out and Breakdown

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. Along the way, the Autobots are ambushed by M.E.C.H., a terrorist organization who wish to steal the nuclear device and use it for their own nefarious purposes. And to make things worse, the Decepticons get involved as well.

Debuts: Silas and M.E.C.H.

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. Upon picking up the message's signal, Starscream and Soundwave capture Wheeljack before he can meet the Autobots, and they send in Makeshift, a Decepticon spy able to take on any form, disguised as Wheeljack to discover the location of the Autobot base.

Debuts: Wheeljack and Makeshift

Deaths: Makeshift

While on a scouting mission in theArctic, Bulkhead and Bumblebee find a crashed space pod buried in the ice. They bring it back to base for examination, and Optimus Prime and Arcee venture out into the Arctic to find clues on the pod's origin. While they are out, the other Autobots discover that the pod contains a large swarm ofScraplets, a vicious and highly dangerous form of Cybertronian wildlife that eats metal. The Scraplets infest the Autobot base, devouring any metal in sight and damaging the Ground Bridge, leaving Optimus and Arcee stranded in the Arctic.

Following Megatron's supposed death, Starscream appoints himself as the new Decepticon leader. However, to his annoyance, he finds that the troops don't respect him as much as they did Megatron and are weary towards him becoming leader. In order to gain their respect, Starscream awakens Skyquake, a legendary Decepticon warrior who was entombed in stasis on Earth for centuries, and attempts to recruit him into his new army. Meanwhile, Ratchet agrees to help Jack, Miko and Rafael with their school science projects, with explosive results.

Debuts/Deaths: Skyquake

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.

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.

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. Meanwhile, Soundwave kidnaps the Autobot-allied human Agent William Fowler, with Starscream wishing to learn the location of the Autobot base.

Debuts: Laserbeak and Terrorcons

Deaths: Terrorcons

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 zombie-like Terrorcons. The Autobots storm an Energon mine in search of their lost comrade Cliffjumper, only to discover that his dead body has been revived as a ravenous zombie by Dark Energon.

Debuts: William Fowler, June Darby, and Decepticon Miners

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.

Debuts: Optimus Prime, Arcee, Bumblebee, Bulkhead, Ratchet, Cliffjumper, Jack Darby, Rafael Esquievel, Miko Nakadai, Megatron, Starscream, Soundwave and Vehicons

Deaths: Cliffjumper