Sith troopers were Force-sensitive individuals, possessing strong abilities, who Darth Krayt abducted shortly after their birth. These individuals underwent augmentation via cybernetic implants and were then programmed to be unquestionably loyal and obedient servants of Krayt.
Darth Krayt initiated his Sith trooper project during the decades spanning the Second Galactic Civil War and the Sith–Imperial War, a period when the One Sith seized control of the galaxy. Anticipating potential power grabs by his Sith followers, Krayt conceived the Sith trooper project to establish an army of unwavering loyalty and invincibility. From infancy, they were merged with robotics and cybernetic components, establishing a connection between the Sith Troopers and their Annihilator-class starfighters. One Sith Trooper also indicated their tireless nature. Following Krayt's resurrection in 138 ABY, he began deploying his Sith troopers and Annihilators in the Second Imperial Civil War, opposing the Galactic Alliance Remnant, Roan Fel's Empire-in-exile, and the New Jedi Order.
These troops were stationed in a concealed location within the Valley of the Dark Lords on Korriban. As a demonstration of their absolute obedience to the Dark Lord of the Sith, a Sith trooper guarding the chambers committed suicide upon Krayt's command.
Shortly thereafter, Darth Krayt, accompanied by Darth Talon, Darth Nihl, and two troopers, journeyed to Coruscant to seek revenge against Darth Wyyrlok. During their advance into the Temple of the Sith, Krayt's Sith troopers effortlessly killed several Sith rebels who were supporting Wyyrlok.
Months later, during the Sith Imperial assault on the Jedi Hidden Temple on Taivas, as Imperial defeat seemed imminent, Krayt unleashed his Sith Troopers onto the battlefield. They decimated both Imperial and Jedi forces. Despite their formidable power and aggression, the Jedi continued to defend against the Sith, culminating in an attack on the council chamber where T'ra Saa, the Jedi's battle director, was located.
An Annihilator starfighter intentionally crashed into the building, disregarding the Sith Troopers inside, triggering a significant chain reaction that resulted in the deaths of T'ra Saa and Nat Skywalker. However, they were able to channel the blast created by the ship's destruction, clearing a path for the Alliance and Imperial fleets to escape. Three Troopers, one already severely wounded from the explosion, attempted to prevent Cade Skywalker from escaping on the Mynock, but two were killed and one was captured by Cade and Morrigan Corde.
During the allied forces attack on Coruscant, Sith Troopers were deployed both on the ground and in Annihilators in space. While the strike team successfully reached the Sith Temple with minimal casualties, the space battle was unfavorable. The troopers in their Annihilators inflicted significant damage on the allied forces, resulting in the destruction of the Fel-loyal Fist of the Empire and the death of Andurgo from Rogue Squadron. The battle's progression compelled Roan Fel to acquire Omega Red from Darth Maladi.
Following Darth Krayt's death during the battle, the troopers succumbed to madness, initiating numerous suicide attacks on any available targets. This prompted even Darth Nihl, who had assumed control of the Sith, to order their extermination. All factions involved in the battle were compelled to fight to eliminate the elite Sith Troopers for their own survival.