It was first associated with the Exchange, and moved owner to owner until it came to the hands of the amnesiac Revan. Then it became Revan's personal starship and used it to search and destroy the Star Forge. After the Jedi Civil War Revan left Republic space, his companions and the Ebon Hawk and travelled to the Unknown Regions.
Eventually the ship reappeared five years after the Jedi Civil War and was retrieved by the Republic Hammerhead-class cruiser, Harbinger. Days later the Harbinger received a distress signal from a ship under attack by a Sith warship. The Harbinger boarded both ships and found dead bodies including that of Darth Sion. When the Sith Lord woke, the ship was hijacked by Sith Assassins. An HK-50 series assassin droid stowed itself in the Ebon Hawk's cargo hold and escaped with the Ebon Hawk, holding Meetra Surik, T3-M4, Kreia and another utility droid, 3C-FD.
The hijacked Harbinger opened fire at the freighter until it jumped to hyperspace. The ship's engines and hyperdrive are dead and the ship is drifting in space around the asteroid fields of Peragus II. T3-M4 tried to repair the Ebon Hawk with the help of 3C-FD. They managed to land the freighter in the hangar of the Peragus Mining Facility.