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You will need to understand Homeworld 1 & 2 lore to understand the following storyline. Please read up.
Following the Vaygr - Hiigaran war and the death of Makaan, the Vaygr scattered and broke into their tribes as they once were, leaving the empire they fought to create in the dust and losing their hyperspace core to the Hiigarans. For two millennia the Vaygr existed like this, fighting against one another, and weakening themselves, with little hope or foresight of a prosperous future. Allowing the Hiigarans to build their great empire.
But during this era of chaos, one great scientist discovered the technology of intergalactic travel, which reached far beyond the capabilities of the united three cores that the Hiigarans possessed. He proclaimed that Makaan would be avenged, the prophecy was false and the Vaygr would restore order to the galaxy. He used his technology to gain control of the tribes and began to forge a new empire. For 50 years the Vaygr united the tribes once again and built up their military. The Hiigarans were unaware of what was happening. A new Vaygr Empire was born with a new culture, purpose, and a powerful military.
The new ideology sat well with many, changing savage tribal conglomerates into a single militant empire and giving the people a purpose. However many Vaygr did not like the restrictions that the new empire placed on their freedoms that they once had. Insurrection broke out and many who supported the old tribal ways rose up to fight the new Vaygr Empire. However their aging ships were no match for the new technologically advanced Vaygr fleet. In every naval engagement the old Vaygr tribal ships stood little chance against the powerful imperial fleet. The rebellion was crushed and Imperial troops began a crackdown to weed out the rebels on every planet in their systems. Most rebels were imprisoned and forced into labor to build the Vaygr fleet, those who escaped fled to Hiigara.
Word of the rebellion reached the Hiigarans and they became aware of the new Vaygr Empire and it’s massive military buildup. They also heard rumours of their new travel technology and feared the worst. The Hiigarans immediately scrambled every warship from every corner of their empire and moved them to guard their systems, however it was too late. The Vaygr had already planted a virus into the Hiigaran’s military network revealing the location of each Hiigaran fleet. The fleets in rout to their defense positions were ambushed by concentrated Vaygr fleets and picked off one by one using their new jump technology until only the last Hiigaran fleet was left.
With little hope of winning the war the Hiigaran’s staged a final defense around their home planet, Hiigara. Here they concentrated their progenitor ships they captured ages ago including the Sajuuk-Khar. The Hiigarans thought that the Vaygr Empire couldn’t stand toe to toe with the progenitor ships in a battle, which was still correct. The Vaygr Emperor knew this and planned carefully to avoid such a battle.
However the Emperor had one trick up his sleeve. Ages ago when Makaan had used his megaships to try to destroy Hiigara he had launched a bomb from his ship onto the surface of Hiigara and buried itself deep underground failing to go off. This bomb was no ordinary bomb, when activated it caused the atmosphere to ignite similar to the atmospheric deprivation weapon used on Kharak by the Taiidan ages ago, but this one was far more potent. However at the time the bomb failed to ignite and Makaan had no time to attempt to shoot an emergency activation signal, as he and his megaships were destroyed by the Sajuuk-Khar.
The Hiigarans were ready and waiting for the massive Vaygr onslaught and were prepared for a long tough battle. Anticipating a massive Vaygr warp into the sector from every direction they formed a defensive ring of ships around the planet concentrating the whole empire’s fleet to defend a single planet.
Then as they anticipated the Vaygr warp into the sector, a single small Vaygr ship entered completely devoid of any crew. Perplexed the Hiigaran fleet commander ordered the fleet to stand down, he then ordered a boarding craft to board the small ship. As the marines prepared to board Hiigaran sensors detected a strong signal originating from the craft. The signal beam was visualized for the commander and appeared to be pointed at a crater on Hiigara, the exact location where Makaan dropped the failed bomb. Before the commander could figure out what happened there was a brief but great flash on Hiigara’s surface, as the flash faded the Hiigaran’s watched in horror as the planet’s surface turned to molten ash and billions of Hiigarans perished in a brief moment.
As the surface smoldered like a dying ember, panic spread among the Hiigaran fleet. There was another flash and there was explosion which fractured the planet and sent debris in all directions. Many Hiigaran ships were destroyed by the debris and at this time the Vaygr Emperor chose to strike. The Vaygr closed in from all directions blocking retreat by using warp inhibitors as well as jamming Hiigaran communications. The Hiigarans defense plan crumbled and every ship fought for themselves or desperately tried to escape.
When the slaughter was finished thousands of Hiigaran ships orbitted in ruin around the fractured planet. At this time the Vaygr Emperor proclaimed his victory to his people. With the destruction of almost the entire Hiigaran fleet he quickly took control of the rest of the galaxy only a few years later, uniting it under his own rule.
For thousands of years after, the Vaygr expanded their ambitions beyond their own galaxy into the infinite void. Vaygr technology grew as they progressed, Vaygr soldiers and crew members were more machine than they were organic. The Emperor even infused himself with cybernetic devices, increasing his intelligence and strength tenfold, as well as making him ageless unbinding him from his ship as he once was. The Emperor placed loyalty programming into his soldiers ensuring his military would never turn on him. In turn he created the most powerful empire in history.
All history of the Vaygr people was lost and the entire species was consumed in the Emperor’s megalomaniacal plans to dominate the entire universe. Empires and nations fell to the Vaygr, entire populations were enslaved and forced to work, strengthening the Vaygr’s military even more. Hope of a freedom was all but lost.
