Over the course of the Rogue Shadow's service, it lost seven pilots.
By the time of Marek's hunt for Rahm Kota, the ship was piloted by Juno Eclipse, with whom Marek would eventually fall in love. She flew the ship to many locations, including the TIE Fighter Construction Facility over Nar Shaddaa, Raxus Prime, and Felucia, all in the course of ferrying Marek to the Jedi Vader had ordered him to destroy.
Later, when Marek was seemingly killed by Vader, the Rogue Shadow was brought to the Empirical for his escape. Eclipse was imprisoned as a traitor, and Marek ordered to leave her to her fate. However, he saved Eclipse, telling her he needed someone to fly the ship. They then began their search for Rahm Kota, who had survived the battle above Nar Shaddaa, following clues from there first to Ziost and then to Cloud City on Bespin. Kota told them that he had a contact in the Senate who had been feeding him information on Imperial targets, but that he first needed to find something on Kashyyyk. There, Galen saved Princess Leia Organa and prevented the construction of a skyhook that would have ferried millions of Wookiees into slavery. Kota then informed the crew of the Rogue Shadow that Leia's adoptive father, Senator Bail Organa, was his contact and had gone to Felucia to find Master Shaak Ti, earlier killed by Marek.
Following the rescue of Bail Organa from the clutches of the fallen Jedi Maris Brood, Rogue Shadow returned to Raxus Prime, where Marek destroyed a Star Destroyer shipyard with an ore cannon. Unfortunately, when PROXY tried to slice into the planet-wide core network, its sentient mind took him over and locked the Rogue Shadow's launch codes, intending to later use it to spread its ideals of order across the galaxy. Marek battled PROXY in a variety of holographic forms before finally defeating the Core and restoring control of the ship.
The Rogue Shadow arrived on Corellia shortly thereafter to witness the birth of the Alliance to Restore the Republic, but it seemed short-lived, as the Empire quickly arrived. After a brief duel, which included the apparent destruction of PROXY, Vader threw Marek from the top of a cliff. Presuming his former apprentice dead, Vader left. Captain Eclipse rescued Marek from the base of the cliff, and the two followed the captives to the Death Star, where Eclipse extracted the Rebels, taking them to Kashyyyk to conclude the formation of the Alliance. Marek, after a pitched battle with Vader and later the Emperor, sacrificed himself to buy them enough time to escape.
Eclipse and Senator Organa later used the ship to return to Corellia to salvage PROXY, presumed destroyed during the attack on the Rebel leaders. The vessel's eventual fate is thus far unknown.