The Third Hyperspace Core was discovered by the Vaygr warlord Makaan and his fleet in the Hethlim Ice Fields as the Vaygr were gaining power throughout the Galaxy. The discovery of the third and final core lead to the "End Time," in which the hunt for Sajuuk, and the reemergence of the power of the once-great Progenitor Empire began.

The Third Hyperspace Core was captured by Hiigarans after Battle in Balcora with Makaan's forces next to nonoperational Sajuuk. Makaan's armadas arrived to Balcora with the help of a captured Progenitor Dreadnaught. Some short time after it made the jump through Balcora Gate, Karan S'jet and her Hiigaran fleet jumped through using the other Dreadnaught. The resulting furious battle was won by the desperate Hiigarans, who managed to destroy the Vaygr Flagship and retrieve the Hyperspace Core from its otherwise obliterated remains.