Ten years have passed since the Armada battles. The Autobots and Decepticons work side by side with humans to harvest Energon. But trouble is brewing with recent attacks by a group of transformers known as Terrorcons. Can the Autobots meet the threat?

The Autobots prepare for the Terrorcons' second strike, but it's not where they expected.

At Desert City, the Autobots fend off the first Terrorcon attack against Earth.

The survivors on Mars are attacked again, but the Autobots must turn their attention elsewhere.

An Energon scout team on a frozen mountain is the target of the latest Terrorcon attack!

At various Cyber Cites the Transformers have set up defensive traps to stop the Terrorcons from stealing Energon. It appears the Autobots have won as their enemies retreat, but as they head back to regroup, Cyclonus, Tidal Wave and Scorponok begin to bicker around Megatron who still lies in his coma. Suddenly, he begins to come to life. Scorponok is outraged at this and whines to Megatron about him stealing all the Energon for himself.

After seeing what Megatron did to Hot Shot, the Autobots end up in a stand off with the Decepticons. Megatron taunts Optimus Prime but allows the Autobots to withdraw without a skirmish. Back at Ocean City, Hot Shot is lowered into an Energon pool for repairs while the Omnicons begin making duplicates of Megatron’s sword. A space bridge is detected near the city and the Autobots fly into action.

A mysterious phantom assassin stalks Optimus Prime. Can Kicker and the Autobots protect Optimus and unmask the assassin before it is too late?

The Decepticons manage to hit Asteroid City and Lunar City at the same time.

The remains of Unicron are finally shown and then the Decepticons attack ocean city only to discover that the Autobots have an Energon tower which activates during the battle. The Energon tower destroys all the Terrorcons and injures for the Decepticons, forcing Megatron to retreat.

Alpha Q prepares to bring Unicron to life, while yet another Energon Tower is secured into place. Below the city, Kicker searches for more Energon with Ironhide, but has trouble because of a similar experience during his childhood. In turn, Ironhide tells Kicker about a legendary transformer named Rodimus, who was an inspirational leader that rallied a group of Autobots to escape the war and create a new world.

A massive attack on Jungle City drives the Autobot troops to carry out a desperate last-ditch plan.

Kicker and the Autobots make a series of startling discoveries amid the ruins of Lunar City.

Megatron has taken yet another plan, to create three meteors from Unicron and propel them at Earth before the Energon grid has been completed. Dr. Jones notices Desert City's Energon tower has a fault, rendering the Energon Grid useless. Meanwhile, the meteors enter Earth's atmosphere, but one is destroyed by Rodimus, aided by more mysterious Blackout drones.

While Snow Cat tests his Hyper Power against the Energon Grid, Megatron decides to go after Alpha Q instead of Earth after finding a Terrorcon spy. On Earth, the Autobots celebrate the Energon Grid, but Optimus calls a conference, telling him the Autobots will have to move their battle into space to defeat Unicron and the Decepticons.

Carlos reports the locators on the two Terrorcons have concluded that the enemy has two bases (Megatron and Alpha Q), while Megatron's plan doesn't succeed as Team Rodimus comes to rescue Scorponok. After the report, Dr. Jones is unveiling a new starship to increase Energon production, named the Miranda II. Optimus reveals their mission is twofold: they are also going to destroy Unicron, and they prepare to set up a space bridge.

Following Kicker's Energon instinct, the Cybertron land on a frozen planet, and soon become stranded.

Escalating tensions reach their boiling point as Optimus Prime and Rodimus clash over difference of their ideals over the menace of Unicron!

Unicron’s body is rapidly reviving, much to Megatron’s delight. Optimus Prime pilots the Miranda II into Unicron’s body in an attempt to destroy it from the inside, but Unicron attempts to crush the Autobots and their ship!

Kicker confronts Alpha Q deep within Unicron, mangning to get the Quintesson to expose his secrets and origins.

As the Autobots scramble to defeat the Decepticons, the sadistic Shockblast is released from captivity on Cybertron.

Several Decepticon spaceships manage to escape Cybertron and arrive at Unicron’s body where Megatron surveys his forces. Over in Unicron’s head, Optimus Prime meets with Alpha Q.

Megatron is plotting to feed Cybertron to Unicron! The Decepticon army is battered and Shockblast forms an elite unit of those few who are intact. Optimus Prime and Rodimus team up and head off to defend Cybertron, leaving Kicker to deal with the injured Alpha Q.

The battle continues on Cybertron as Optimus Prime and Rodimus once again act as one team. The Decepticons are able to cause more tears in the Energon grid, allowing Megatron to swoop down with the Terrorcons, bent on stealing the Energon from the core.

Megatron and Optimus Prime are set to face off in a final showdown - until Shockblast interferes.