[2] Ten years after the war for the Mini-Cons and the apparent destruction of Unicron, the mysterious Alpha Q (which stands for "Quintesson"), operating out of the husk of the planet-eater's body, releases energy-eating Terrorcons to attack the Autobots' Cybertron Cities in the Solar system, gathering Energon for Alpha Q's plan.

As the Autobots mobilize against the new threat alongside their human allies (including the teenager Kicker), Alpha Q creates Scorponok to lead the Terrorcons and forges a sword from the Spark of the Decepticon leader Megatron (whose corpse lies within Unicron), later known as Galvatron, in order to turn the other Decepticons on Earth to his side.

Meanwhile, as the Autobots begin construction of Energon Towers to protect the Earth, the legendary figure from Cybertron history known as Rodimus makes his reappearance.

The Autobots form an alliance with Alpha Q, who is already working with Rodimus and his crew, and learn his origin and his motives for stealing Energon: he seeks to use it to recreate that which Unicron has destroyed.

In the ensuing battle, the rupture of several Energon Towers sees a blanket of damaging Energon gas coat Cybertron's surface, keeping the Autobots trapped off the planet, forcing them to send in Kicker and the Omnicons to stop the gas flow while Galvatron seizes control of the planet and directs its movement back to Alpha Q's region of space.

In a multi-pronged attack, the Autobots turn the tables, but Galvatron then immerses himself in the Super Energon again, growing to a colossal size, as Unicron's mind once again takes over his own and directs him into space to merge with his Spark, still intact in the void.

Galvatron then seeks to destroy Unicron's spark, but is possessed by it, while all of the Autobots combine their Sparks of Combination with Optimus Prime, reviving him and leading into the final battle with Unicron, which is promptly aborted when Galvatron takes control of his body again and plunges himself into the foundling sun created by Primus from the Super Energon, preferring to die than to be manipulated.

The cast of Superlink was:[citation needed] Such as with the previous line of Transformers: Armada, the Energon toyline came with its own mini-comic/toy catalogue with a brief five-page story told in multiple languages one after the other; most of them formed parts of an arc, whilst others featured back and forth victories between the Autobots and Decepticons, whilst showcasing the new additions to the line such as the Terrorcons and Omnicons.

Rad and Alexis would get more time, sans Carlos, as the storylines progressed, with both showing a deeper affection for the other, however the relationship was never fully explored due to the closure of Dreamwave.

The Transformers presence on Earth was also handled with more resentment and hostility from a handful of citizens; this culminated in a large-scale Terrorcon assault on Earth during the second story arc, as Megatron transported Optimus into the hub of Unicron, where his spark had been trapped since the conclusion of the Armada comic, and manipulated Prime into freeing him so he could enter a body he had been secretly preparing.

This led to much more solid, stable and sturdy-looking robot modes, but the entire line performed poorly, so it was dropped in its entirety in 2004.