Dark Energon was so rare on Cybertron that it was practically non-existent.Cue Vincent Price voiceover.
When Megatron returned from deep space after three years away, he revealed he'd found a new way to win the war: Dark Energon, a substance rumoured to be the blood of a power full enemy and possessing the power to raise the dead. A test with the corpse.proved it could indeed do this, turning the dead into berserker zombies; it could also turn machinery into animalistic robots, and merely touching it could render a Transformer ill. Megatron, being Megatron, thought it'd be a jolly good idea to shove some into his own spark. He survived and began to gibber and rant about the power and how it was like he could hear Unicron's thoughts...
Optimus Prime recognised what Dark Energon was, and rachet was stunned to learn that's what they were facing. They went to the site of an old Transformer battle, knowing Megatron would plan to raise the fallen as an undead army with the Dark Energon... but got there too late to stop the tyrant! space bridge, they realized Megatron intended to reawaken Cybertron's fallen soldiers, and send them to destroy Earth. Megatron threw his store of Dark Energon crystals into the space bridge, but before the Terrorcons could cross the space bridge, the Autobots sabotaged it, causing it to collapse on itself, taking Megatron and the Terrorcons with it.Megatron showed off by sending waves of Terrorcons to exhaust the two, and then revealed that was not his endgame. Discovering the Decepticons had built a
Luckily for Megatron, his Dark Energon infusion kept him alive until Starscream found him floating in space. Discovering the cause of his survival, Starscream ripped the Dark Energon crystal out and prepared to leave Megatron to die, only to have to take Megatron back to the ship when Soundwave's deployer discovered them.
Megatron escaped from his own body into Bumble Bee's, and made him recover the Dark Energon crystal he had used to create the Terrorcon during the battle with Optimus and Ratchet, thereby facilitating his own body's revival.
While Megatron had revived himself, he had forgotten that Starscream possessed the original shard of Dark Energon ripped from him. Now back in a subordinate position, Starscream's previous opposition to using Dark Energon to raise an undead army vanished when he tried to raise Skyquake from the dead. Starscream broke the shard in half, one to raise Skyquake, the other to achieve symbiosis. While it managed to raise Skyquake, the new Terrorcon became trapped in the ShadowZone, depriving Starscream of his new warrior.
Following this time, Megatron angrily commented that his vision for Dark Energon was to give him an unstoppable army of the undead to command and conquer the cosmos. However, he was relegated to only holding a small piece that now still animated his spark and thus became determined to locate more. As such, he ordered his Decepticons to gather components for a new Space Bridge so that he could use it to find more Dark Energon. He also attacked Bumblebee and wounded raff who became infected with Dark Energon which Ratchet was forced to expel by using normal Energon to counteract its effect. Megatron also became plagued by visions of a dark figure and a volcano site.
Traveling alone to the site, he believed that the volcano on Earth was the location where his new Space Bridge would bring him a new source of Dark Energon from space. This led in a confrontation with Optimus Prime where Megatron eventually gained the upper hand. At the climax of the battle, a large deposit of Dark Energon erupted from the volcano to which a delighted Megatron learned that it was not to come from space from the planet Earth itself. This left a confused Optimus Prime to wonder about Dark Energon come from beneath the planet with the event coinciding with the tale told by the Ancients in the Covenant of Primus. The Dark Energon eruption was later determined to be pumped from Unicron himself, as he awakened in the Earth's core.
The Nemesis still had stocks of Dark Energon on board when it crashed. Megatron used some to reactivate the warship's power core, only to discover that as a side effect, he had awoken an intelligence which controlled the ship. The warship's mind only returned to dormancy when the Dark Energon was extracted from the power core.