During the Cold War that occurred between the Galactic Republic and the re-established Sith Empire, Imperial Intelligence tasked their operative Cipher Nine with a lengthy pursuit of a terrorist known as the Eagle. This mission was initiated after the Eagle's organization annihilated the Dominator, which served as the flagship for Dark Council member Darth Jadus.
News spread that Darth Jadus, along with thousands of dignitaries, Sith, and slaves, had perished when the Imperial dreadnought Dominator was destroyed during a tour of Imperial territories. Shortly after this event, a message was broadcasted throughout the Empire by a terrorist leader known only as "The Eagle," a former Imperial starfighter pilot and a veteran of the Great Galactic War. The Eagle took responsibility for the destruction of the Dominator, and claimed to have allies on numerous planets. To investigate further, Keeper instructed Cipher Nine to track down and eliminate the Eagle's key terrorist associates and financial backers. Before commencing this mission, Nine was summoned to the Sith Academy on Korriban to meet with Darth Zhorrid, Jadus' daughter, apprentice, and successor, before the Agent started the hunt for the Eagle. The first assignment took place on Balmorra, which was in the midst of a brutal civil conflict. Nine's target was "Gray Star," an associate of the Eagle who was allied with the Balmorran resistance. Sanju Pyne, an Imperial agent embedded within the Resistance, aided the effort, resulting in Gray Star's demise. On Nar Shaddaa, a retired agent named "Watcher X" assisted in the destruction of a chemical factory used by the Eagle to produce "Cyclone," a potent stimulant used to enhance his soldiers' strength. Watcher X, who was being held in the Shadow Town prison, capitalized on the power disruption caused by the factory's destruction to escape his confinement.
Following the destruction of the factory on Nar Shaddaa and as Nine prepared to depart, communication with Watcher Two was interrupted by Darth Zhorrid. She instructed the Agent to return to Nar Shaddaa to find Vyord Yanol, the last individual believed to have seen Darth Jadus alive. As the Agent pressed him for information, Yanol panicked and drew a blaster. Despite Zhorrid's orders to capture him alive, Nine killed Yanol, which led to a furious condemnation (including a slap) from Zhorrid upon the Agent's return to Dromund Kaas. Resuming the hunt, Watcher Two revealed an intercepted message from the Eagle describing "Eradicators," techno-organic satellite weapons capable of large scale destruction, and his threat to use them against the Empire. This led the Agent to Tatooine and the "Ghost cell," a nearly mythical group of assassins that provided training to the Eagle's terrorist network. With assistance from Mia Hawkins, Nine eliminated the Ghost cell and killed its leader, known only as "the Old Man."
Ultimately, the trail led to Alderaan, which was also engulfed in civil war. The target was a former nobleman named Denri Ayl, who acted as an intermediary between the various houses of Alderaan. After meeting with Diplomatic Service emissary Vector Hyllus, who had become a Killik Joiner during his time on Alderaan, Nine went to House Cortess, allies of the Empire-backed House Thul. Despite initial resistance, Nine secured an audience with the Cortess leaders, Baron Peyar and Baroness Chay. With Hyllus' help, Nine infiltrated the stronghold of House Alde to verify that Ayl was the financial backer of the Eagle's terrorist network, and then tracked Ayl to House Rist. However, after killing him and examining Ayl's logs, Nine discovered that Ayl's attempts to enlist the services of the Rists, a family of renowned assassins, had been initiated by Baroness Chay herself. The Cortess estate possessed sufficient shielding and weaponry to withstand an attacking army or a Killik swarm, forcing Nine to find an alternative entry method. Aided by Hyllus and his Killik nest, Nine infiltrated the Cortess estate's power generator, which was concealed in the Glarus Valley, and utilized Killik larvae to destroy the generators before attacking the estate itself. Upon entering the throne room, Baron Peyar surrendered, and the Baroness was killed by Captain Perovius, the head of the Cortess House Guard. Although the actual traitor was dead, Nine condemned the remaining members of the House to death, leaving the Cortess estate to Hyllus' Killiks to establish a new hive.
With the Eagle's support network dismantled, Watcher Two informed Nine that the Eagle's location had been identified as the "Eagle's Nest" on Hutta. After infiltrating the base and fighting through the Eagle's forces, Nine confronted the terrorist leader, who revealed that his benefactor was someone within the Empire itself. The Eagle's computer contained only half of the command codes for the Eradicators; the other half was in the possession of his Sith patron. If the complete code was not transmitted within a specific timeframe, the Eradicators would activate randomly and attack indiscriminately, rather than targeting designated locations. With all the necessary information acquired, Nine killed the Eagle and returned to Dromund Kaas.
Keeper then sent Nine and Watcher Two to the Artus system, an uninhabited system within Imperial territory. It was believed that a Harrower-class dreadnought orbiting Artus Five contained the second half of the Eradicator codes. They boarded the dreadnought, which was crewed only by crazed Imperial soldiers and droids, and discovered that it was emitting a jamming signal to prevent them from calling for reinforcements. While Watcher Two guided the Agent via a communicator implant, Nine was tasked with reaching the bridge and using the complete command codes to deactivate the Eradicators en masse. Upon reaching the dreadnought's bridge, Nine was shocked to find Darth Jadus, very much alive, accompanied by two cybernetically enhanced dark guardians.
Speaking in his emotionless, mechanical voice, Jadus revealed that he had orchestrated his own death as part of a scheme to cleanse the Empire of its "corrupt" elements, especially the Dark Council, and to usher in a new era of terror, with the Eradicators serving as his secret weapon to eliminate his rivals. He invited Nine to join him as his chief agent in this new order. As Jadus explained his plan, Watcher Two secretly communicated over the comm implant, explaining that to maintain Jadus' focus, Nine would need to activate the Eradicators, resulting in thousands of deaths, before Jadus could be stopped. After activating the Eradicators, Nine swiftly deactivated the jamming signal and sabotaged the ship's shields and hyperdrive, preventing it from escaping. Watcher Two managed to summon reinforcements, including three members of the Dark Council, leaving Nine to confront Jadus alone. Despite Jadus' Force abilities being second only to the Emperor himself, Nine withstood Jadus' attacks while diverting necessary power for Watcher Two to trap Jadus in a ray shield, holding him until reinforcements arrived. Ultimately, Jadus was forced to surrender and was handed over to the Dark Council.
The Eradicator incident triggered a major upheaval within the Imperial government, leading to the removal of several officials, including the Minister of Intelligence. Keeper was appointed as the new Minister of Intelligence, reporting directly to the Dark Council; Watcher Two succeeded him as the new Keeper.