Megatron's presence in Transformers: Energon initiates with his apparent destruction at the conclusion of the preceding series, his corpse resting within the dormant Unicron. The entity Alpha Q fashions a sword from Megatron's Spark to command the loyalty of Earth-based Decepticons. Megatron engineers his own resurrection, seizing control of Unicron's body and forcing Alpha Q to flee into Unicron's head. Using Unicron, Megatron directly assaults Earth, specifically targeting Ocean City. Alpha Q counters by recreating Starscream as an assassin to eliminate Optimus Prime, but Starscream is instead brainwashed into serving Megatron. Scorponok, ostensibly serving Alpha Q, operates as a mole within Megatron's Decepticon ranks. Megatron mobilizes Unicron's reanimated body to pursue the Autobots through a space bridge, emerging near Cybertron. The planet, fortified with Energon towers, fires on Unicron, inflicting significant damage. During this conflict, the Decepticon criminal Shockblast joins Megatron. Guard Wing Dagger is recreated by Primus as Wing Saber after his partner Padlock dies during Shockblast's escape. Megatron reconstructs his damaged follower Tidal Wave into Mirage. Megatron ultimately succeeds in fully animating Unicron, reclaiming the head section and killing Alpha Q. Shockblast attempts to seize control of Unicron, but the planet-eater's consciousness overthrows his mind, destroying Shockblast. Megatron resumes command but struggles against Unicron's influence as their minds battle for dominance during a clash with Optimus Supreme. Following Unicron's physical destruction, its consciousness persists within Megatron. After many Decepticons are captured and imprisoned on Cybertron, Megatron leads an assault to free them. Shockblast's brother, Sixshot, joins the Decepticons seeking revenge on Optimus Prime. Guided by Unicron's lingering consciousness, Megatron discovers a subterranean reservoir of Super Energon. Immersing himself in this substance transforms him into Galvatron. This transformation awakens two guardians of the Super Energon – Bruticus Maximus and Constructicon Maximus – who side with Galvatron. The third guardian, Superion Maximus, allies with the Autobots. Galvatron coats Cybertron's surface in damaging Energon gas, trapping the Autobots off-world. He seizes control of the planet and directs it toward Alpha Q's recreated worlds. The Autobots eventually turn the tide, but Galvatron immerses himself in the Super Energon again, growing to colossal size as Unicron's mind fully takes control, directing him to merge with Unicron's Spark in space. Optimus Prime also grows to gigantic size, confronts Galvatron, and drains Unicron's essence from his body. Galvatron attempts to destroy Unicron's Spark but becomes possessed by it. All Autobots combine their Sparks of Combination with Optimus Prime to revive him. Galvatron briefly regains control and plunges into a nascent sun created by Primus from the Super Energon, choosing death over continued manipulation. This act ignites the sun, revitalizing Alpha Q's worlds. In supplemental media like toy pack-in comics, Megatron sends forces such as the Divebombs or Insecticons to absorb Earth's Energon or directly battles Optimus Prime. He observes significant events, including the appearance of Optimus Prime's duplicate, Grand Scourge, with interest. These materials depict his relentless pursuit of power and confrontations with the Autobots, culminating in his transformation and sacrifice.