Ten years after the war for the Mini-Cons and the apparent destruction ofUnicron, the mysterious Alpha Q (which stands for "Quintesson"), operating out of the husk of the planet-eater's body, releases energy-eatingTerrorconsto 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 createsScorponokto lead the Terrorcons and forges a sword from the Spark of the Decepticon leaderMegatron(whose corpse lies within Unicron), later known asGalvatron, in order to turn the other Decepticons on Earth to his side. Megatron engineers his own resurrection, however, taking control of Unicron's body and forcing Alpha Q to flee inside Unicron's head, then attacking Ocean City on Earth. Alpha Q recreatesStarscreamto assassinateOptimus Prime, but Starscream is brainwashed into Megatron's service, all along Scorponok continues to act as Alpha Q's mole within the Decepticons. Meanwhile, as the Autobots begin construction of Energon Towers to protect the Earth, the legendary figure from Cybertron history known asRodimusmakes his reappearance.
With the activation of Earth's new Energon Grid, shielding it from attack by the Decepticons, the Autobots turn their attention to Unicron. Leaving Earth in the ship, theMiranda II, they locate Unicron's body. Megatron mobilizes the chaos-bringer, and pursues the Autobots through their space bridge, emerging in the vicinity of Cybertron. The Transformers' homeworld riddled with Energon towers, fired, leaving Unicron badly damaged. 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. Meanwhile, Megatron's forces attack Cybertron, and the Decepticon criminal Shockblast is inducted into their ranks. In the course of Shockblast's escape from prison, guardWing Daggerswears revenge for the death of his partner, Padlock, and when an Energon tower collapses on him and Tidal Wave, Megatron reconstructs his minion as Mirage, while Primus recreates Wing Dagger as the mighty Wing Saber, who joins the battle alongside Optimus Prime within Unicron. As the battle rages, Kicker arranges to channel all of Earth's Energon into Unicron's head, which Alpha Q then rams into Unicron's body. The resultant reaction with the negatively charged Energon within the body causes a fissure in reality, through which all the combatants are sucked.
In the new region of space on the other side of the fissure, Alpha Q has successfully recreated all the worlds destroyed by Unicron, sustaining them from within Unicron's head, which has now become an Energon sun. The Autobots set about establishing Energon Towers on the new planets to protect them, while Megatron sees the new worlds as a source of more Energon to reactivate Unicron. Having brainwashed Scorponok to become fully loyal to him, Megatron attempts to do the same to Inferno, but he fights the process. A rescue team consisting of Cliffjumper, Downshift, and Bulkhead is dispatched from Cybertron and Earth and teams up with the Autobots to protect the new worlds, but Inferno is then destroyed when he falls into the Energon sun, defeating the Decepticon influence of Megatron. Thankfully, his Spark is saved and he is reborn as Roadblock, just as the ancient Autobot, Omega Supreme, is awakened on Cybertron and joins the Autobots. Megatron succeeds in animating Unicron, who reclaims his head, killing Alpha Q in the process, but then Shockblast attempts to seize control of Unicron, only to have his own mind taken over by the "demi-god", ultimately destroying him. Megatron then resumes control, but falls prey to Unicron's influence as well, as the two minds battle for control as they struggle with Optimus Supreme, the combined form of Optimus Prime andOmega Supreme. Optimus Supreme is enlarged to giant size with a power boost from Primus which also energises several of the other Autobots. In a veritable battle of the titans, Optimus Supreme destroys Unicron, but his mind lives on within Megatron.
Although many of the Decepticons are captured and imprisoned on Cybertron, Megatron and his remaining forces soon attack the planet and free them. Another fugitive is Shockblast's younger brother, Sixshot, who joins Megatron's team to get revenge on Optimus Prime for his brother's death. Guided by Unicron's consciousness, Megatron is led to a subterranean reservoir of Super Energon, which transforms him into Galvatron. Two of the Super Energon's guardians, Bruticus Maximus and Constructicon Maximus, awake fromstasisand side with him, but the third, Superion Maximus, sides with the Autobots. 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. Optimus Prime grows to gigantic size also and forces Galvatron into a battle, bringing his consciousness back to the surface, at which point Prime drains Unicron's essence from his body. 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. With this action, the sun ignites, breathing new life into Alpha Q's worlds, lighting the way to a brighter tomorrow.