After the Jedi Civil War, the Harbinger was assigned to patrol several regions of Republic space, one of a scant few ships left to do so. In 3951 BBY, the ship was en route to Onderon to deal with the unrest on that world when it was ordered by Admiral Carth Onasi to divert its course to the Outer Rim. Admiral Onasi gave the mission highest priority, and though the captain had doubts about it, Harbinger soon picked up a passenger—Meetra Surik—recently returned from outside Republic space. With its new passenger onboard, the Harbinger then set a course for Telos IV, intending to reach the world within ten days. It was meant to aid in the recovery effort on that world.
One of the beings aboard the Harbinger had other plans however, an HK-50 assassin droid posing as a protocol droid, one of many scattered across the Republic fleet. The captain asked HK-50 to keep watch on Surik, and the droid complied, though for its own motives.
Admiral Carth Onasi, during a holorecording with the captain of the Harbinger.
On its way back to Telos, the Harbinger picked up a distress signal coming from a freighter, indicating that it was under attack by Sith forces. Since they could not match the ID signature of the vessel to their own databanks, the Captain of the Harbinger forwarded it to the Republic and requested permission to investigate. Admiral Onasi recognized the freighter as a ship he had once traveled on, the Ebon Hawk, and gave permission to the captain of the Harbinger to divert his course. Once it had investigated the Sith presence and found all it could on the Ebon Hawk, the Harbinger was to resume its course for Telos.
The Harbinger found the Ebon Hawk and a Sith warship when it arrived. Attaching an umbilical to the Sith ship, they dispatched three strike teams to investigate it. An initial sweep turned up no one. This was, in fact, because the ship had held Sith Assassins, who possessed stealth abilities and were therefore able to cross back into the Harbinger without being detected. The sweep later uncovered another passenger of the Sith ship—a seeming corpse, its body displaying thousands of fractures and scars. The medical technicians of the Harbinger were unable to determine whether it was alive or dead, and so it was placed in a kolto tank.
As for the freighter, an initial sweep of it turned up nothing but a T3-series utility droid and several corpses. When the crews turned up nothing else, the Harbinger tractor beamed the Ebon Hawk over to itself. It, too, brought an unexpected passenger—Kreia. The Sith had been busy in the meantime. Crewmen began missing shifts, some were unable to be reached on the comm, and some even felt that they were being watched. The medical officer prepared to perform autopsies on the corpses recovered from the Hawk.
The already-compromised Harbinger then received another blow. HK-50, intending to capture Surik for the crime lord G0-T0, had arranged for a cascade failure in the ship's communications, weapons, and engine systems. The Harbinger was left crippled, drifting through space. Surik, meanwhile, had been administered an excessive dose of sedatives during a routine medical examination, and HK-50 stashed the unconscious Jedi in the ship's cargo compartment, intending her to remain there until the help he had summoned arrived. Kreia, however, boarded the Harbinger in search of Surik. She found her in the cargo hold, and took her aboard the Ebon Hawk. HK-50, recalculating his plan, joined them.
Darth Sion on the Harbinger's bridge
The Sith "corpse" had meanwhile proven to be quite alive—it was in fact a Sith Lord, Darth Sion, who burst from his kolto tank and announced his desire to take Surik. The bridge, alarmed, sent a security team to the medbay, but they were quickly killed. Sion went in search of more of the Harbingers crew, and his Assassins began decloaking and joining him. The Sith soon seized control of the vessel, and as the Ebon Hawk pulled away from the Harbinger and the Harbingers systems began to go critical, the capital ship fired on the freighter, hitting it as it leapt to hyperspace.
As for the captain, he, along with his officers and crew, was killed when Darth Sion's Sith seized control of his ship.
After the Harbinger docked with the Peragus Mining Facility, Surik was able to piece together some of the events that took place from logs kept by the Captain, among other officers.