VIOLEN JYGAR
Violen Jygar, the Phantom Emperor of Chaos, was an ancient, alien being who lived in the deepest realms of space. In an older life, he was three separate entities-Vion, Igren, and Lenja-until they were fused into one being by unknown means. He was seen as a threat by the first thirteen Transformers and they set out to defeat the Phantom. They eventually succeeded in doing so, and Jygar was left as a weakened, faint spirit.
Millions of years later, during the Great War, the many sparks and corpses of deceased Destrons and Decepticons joined together and recreated the Phantom Emperor's body. After Unicron's second defeat at the hands of the Autobots, Violen Jygar found Galvatron and gave him the idea of merging with Cybertron's core and becoming the planet itself. This was a ploy, however, in order to get Cybertron into its long forgotten robot form so that Jygar to transfer his spirit into it. While he did succeed in transferring his spirit, his triumph was short-lived as the Autobot Rodimus Prime was briefly given a giant body by the Matrix, which was used to destroy Violen Jygar and return Cybertron to its planetary state.
Despite his apparent death, some of the elder Autobots and the original Thirteen theorize that Violen Jygar lived on in some form, and that more sparks of deceased Decepticons would come together again and allow the Phantom Emperor to rise once more.
JHIAXUS AND HIS EMPIRE
Jhiaxus was a Guardian scientist who served under Nova Prime near the end of the Destron War. When Nova took off on the original Ark to begin his Expansion, Jhaixus accompanied him and, unwittingly, ended up in the Dead Universe. There they encountered the Fallen, who convinced Nova and his companions to join him.
Millions of years later, Jhiaxus assisted Nova in carrying out the Expansion and to absorb Earth's Sun. He sent various minions such as Grindcore to stop the Autobots from intervening, though they all failed. After Nova was seemingly killed, Jhaixus retreated from the Dead Universe and went into hiding.
During his exile, Jhiaxus crossed paths with the Liege Maximo, a brother of the Fallen, who presented an alternative to Nova's plan. Instead of conquering the universe by torturous means, he should instead conquering, it should be conquered by brute force, or, in Maximo's mind, an invasion.
Thus, Jhiaxus formed the Cybertronian Empire out of the remnants of Nova Prime's followers, as well as renegade Decepticons. He then began conquering numerous worlds, including Gorlam Prime and the Galactan system. He then led his forces to Cybertron, launching a devastating invasion that nearly saw the empire victory. At the last minute, however, Rodimus Prime sneaked onto Jhaixus' flagship, the Twilight, and used the Matrix once more to wipe out the Cybertronian Empire. While the Matrix did destroy the empire, Jhaixus managed to survive along with Rodimus via a portal and mysteriously vanished.
It is unknown if Jhiaxus escaped the portal, nor where he escaped to.
SHOCKWAVE
Out of all of the villains the Autobots have encountered during their adventures, Shockwave is the most clever and deceiving. Before the Great War, he was a pupil of Jhiaxus during Nova Prime's age shortly before the Guardian leader took off to start his Expansion plan. When the Autobots were formed, Shockwave became High Governor of Tarn.
Years later, Shockwave discovered of the Decepticon uprising and decided to join the new faction, becoming one of Megatron's top lieutenants. When Megatron left to pursue the Autobots led by Optimus Prime, he left Shockwave in charge of the Decepticon forces on Cybertron.
Four million years later, after Megatron's return and later imprisonment, Shockwave took command once again during a brief Decepticon civil war, leading Megatron's most loyal followers. When Megatron returned as Galvatron, Shockwave mysteriously vanished.
During the Unicron conflict, Shockwave expanded on a plot he devised during his temporary reign over the Decepticons; a plot to overthrow Megatron. He gathered a small group of Decepticons who were disloyal to Megatron and launched an attack on Cybertron in order to draw out Galvatron so that he could destroy them. Shockwave was defeated however, and he decided to take his followers to Axiom Nexus, a multiversal hub for all Transformers. While he succeeded in taking over the vast city, he was unable to taking his enslaved forces to Cybertron due to Starscream blocking out all paths out of the city.
Years later, the ancient being Necros Prime arrived in Axiom Nexus and offered Shockwave to let him help in finding a way out of the city, which Shockwave accepted. However, once Necros had created a portal exit, Shockwave attempted to kill Necros. His attempt failed and he was savagely beaten by the Prime. As a sort of punishment, Necros sent Shockwave away to an alternate universe based on the Pixar movies.
While in the Pixar-verse, Shockwave brought together two ultimate plans. One was to create a new body out of parts from the Axiom ship so he could strike fear in the humans' hearts and enslave their world. This plot was foiled as well by the Autobot team led by Optimus Minor, who captured Shockwave and sent him back to their universe's Cybertron.
Shortly after his capture, Unicron's Abduction began, setting the stage for Shockwave's next plan; to merge Unicron with Cybertron and use the Chaos Bringer's body as a vessel to conquer the universe. He used the Decepticons led by Megastorm to stall the Autobots long enough to bring Unicron/Cybertron into Earth's orbit. He then traveled into Unicron's core so he could replace Unicron's spark with his own. He was prevented though by Optimus Minor (or Orion Pax) and Megastorm, the latter who finally killed Shockwave by shooting him through the chest.
Shockwave's death and Unicron's final demise would unwittingly bring an alliance between the Autobots and Decepticons and an end to their war.
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