
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.

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. 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.

There, Galen saved Princess Leia Organa and prevented the construction of a skyhook that would have ferried millions of Wookiees into slavery. 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. 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. However, Marek saved Eclipse, telling her he needed someone to fly the ship. Eclipse was imprisoned as a traitor, and PROXY suggested to leave her to her fate.

Later, when Marek was seemingly killed by Vader, the Rogue Shadow was brought to the Empirical for his escape. 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. 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. According to Starkiller's clone's memory, another was a sergeant Vader killed because of tardiness. According to PROXY, one of them was killed by a Corellian gunrunner after assuring Starkiller that he could take care of himself. Over the course of the Rogue Shadow's service, it lost seven pilots. It was piloted by Juno Eclipse, Galen Marek's eighth pilot. Perhaps the ship’s most impressive feature, however, was its experimental stygium crystal cloaking device, which could keep the vessel hidden from even the most powerful scanners for short periods of time. It also had the fastest sublight engines in the Imperial fleet. The vessel boasted an advanced hyperdrive, cutting-edge sensory arrays, a fully functional medical bay, crew quarters, a workshop and a meditation chamber that could double as a training room. It also shared certain design elements with other Imperial craft, such as the Eta-2 interceptor and the starfighters of the TIE series.

Built by Sienar Fleet Systems, Rogue Shadow's design was based on that of Scimitar, the Sith Infiltrator employed by Darth Maul.
