The Temple of the Sith, which originated as the new Jedi Temple, was a structure situated on the planet Coruscant. Having been the base of operations for the New Jedi Order from the conclusion of the Yuuzhan Vong War onward, it fell to the control of the dissenting One Sith in the year 130 ABY. Subsequently, it was retaken by the New Jedi Order in conjunction with the restored Galactic Alliance at the termination of the Second Imperial Civil War in 138 ABY.

In the year 130 ABY, the New Galactic Empire was seized by Darth Krayt and his adherents, the One Sith. The New Jedi Temple was captured, and the edifice was renamed the Temple of the Sith and underwent significant reconstruction. The symbolic transparisteel pyramid was dismantled, and the roof was redesigned. Mirroring the ancient Temple, four towers were erected at each corner, while the New Jedi Order's supplementary four pyramids were demolished.
Alterations in the height of neighboring buildings resulted in only the newly exposed pyramidal roof being visible. The Precinct, along with the Temple Ziggurat, were obscured from sight, while the formal entrance was established on the roof, and the Processional Way was reconstructed as an elevated bridge spanning the former road. Given that only the upper section of the Temple was rebuilt, the foundations and portions of the interior configuration were easily accessed by Cade in 137 ABY.
Darth Maladi established her laboratory within the section previously dedicated to healing practices and scientific inquiry. It was within this space that she interrogated Hosk Trey'lis in an attempt to ascertain the whereabouts of Cade Skywalker, thus initiating the sequence of events that culminated in the last Skywalker's capture. Krayt detected Cade Skywalker's entry into the Temple of the Sith with the intention of rescuing the Jedi Hosk Trey'lis. Krayt commanded his Hands, Darth Nihl and Darth Talon, to apprehend Skywalker and bring him before their master. Cade infiltrated the Temple utilizing one of the original entrances, and ultimately liberated the Bothan Jedi healer.
Subsequent to his capture by the Sith Hands, Cade was delivered to Darth Maladi for purposes of torture. Employing a fatal dosage of ixetal cilona, she intended to manipulate him into a pliable state, but her endeavors were thwarted due to Cade's prior consumption of death sticks and his substantial Force abilities, which significantly augmented his resistance to the poison. Upon learning of this, Krayt sought to recruit Cade into his ranks, but Cade declined. In a display of cruelty, Krayt instructed Maladi to infect the recently captured Jariah Syn and Deliah Blue with lethal Yuuzhan Vong Yorik-Kul coral seeds. Cade rescued his companions and negotiated an agreement with Krayt: he would remain with the Sith in exchange for his friends' liberation.

Krayt proceeded to indoctrinate Cade and recounted to him, Darth Talon and Darth Wyyrlok, the narrative of A'Sharad Hett, a Jedi who transitioned to the Sith. Hett was, in fact, Krayt, as Skywalker came to realize. Eventually, Skywalker embraced what Krayt perceived to be his predetermined path and consented to study the ways of the Sith. Krayt instructed him to heal Talon, as she would serve as his instructor. During Cade's training, Talon would escort her apprentice to the Sith Art Chamber and the basement, where they would engage in combat with dilapidated droids and Yuuzhan Vong growths. Concurrently, Imperial agent Morrigan Corde infiltrated the Temple and strategically placed a series of Yuuzhan Vong bugs within the antiquated power core. Skywalker underwent training as an acolyte, compelled to heal himself even from the most minor of injuries.
Following a failed attempt to once again rescue Hosk Trey'lis from Maladi's laboratory, Darth Krayt commanded Cade to execute the Jedi Master. Cade refused, prompting Krayt to execute Trey'lis himself. Incited by Krayt's ruthlessness and emboldened by the Force-ghost of Kol Skywalker, Cade employed the Force to shatter a display case containing his father's lightsaber and subsequently engaged the Sith in a duel. He then utilized the weapon to stab Darth Talon in the abdomen, immediately incapacitating her. He was then attacked by Darth Nihl. Krayt remained at a distance, attempting to persuade Cade to slay Nihl in a fit of rage and embrace the Sith path. Ultimately, Cade severed Nihl's arm, hurled him against a wall, and unleashed Force lightning upon him. Krayt then urged Cade to avenge his father's demise by killing Nihl. As Cade and the Sith engaged in a dispute, the Mynock, which was initiating its attack, was intercepted by Skull Squadron; however, Morlish Veed instructed Moff Rulf Yage to cease the assault, citing that the Sith had mandated that the Temple's airspace remain undisturbed. Unbeknownst to Yage, this entire sequence of events had been prearranged to ensure Cade's rescue. As the Mynock reached its intended location, Corde detonated the Vong bugs, resulting in the destruction of the Temple hangars.
At the precise moment when the duel between Skywalker and Emperor Krayt was reaching its zenith, Morrigan Corde shattered the window behind them, showering Krayt with transparisteel fragments. Cade then leaped out and was rescued by Jariah Syn aboard the Mynock, who pulled him inside. The Mynock then fled the planet and entered hyperspace, but not before Corde revealed her identity to Cade via a comlink. Corde disclosed that she was his mother, but when Cade demanded explanations, she retorted that he would receive none.
Upon the Sith's acquisition of the Temple, they commenced the gradual removal of vestiges of the former Order. The transparisteel pyramid that topped the ziggurat was dismantled, exposing the stone pyramid that had been constructed around the Sacred Spire. Portions of the pyramid were reinforced with durasteel armor, while expansive crimson-colored windows were installed in every chamber and hall. The summit of the mountain was removed, and a gaping aperture at the apex of the pyramid emitted a perpetual column of smoke. Labyrinthine and shadowy, the meandering corridors of the Temple were tinged red by the flames of distant torches, establishing a fiery ambiance throughout the complex. Statues of deceased Sith Lords towered into the darkened heights of the Temple, while bridges traversed what appeared to be bottomless chasms. Mold proliferated on the lower-level stairs and walls, while Dianoga began to infiltrate the unkempt, flooded halls. Combat droids patrolled the dismal halls, lying in wait to ambush unsuspecting Sith acolytes, ensuring that occupants of the Temple remained perpetually on edge and wary of attack. With the Temple Ziggurat obscured from view, a new entrance was constructed on the roof of the Temple, which now served as the base of the Sith Pyramid. Simple and devoid of symbolism, the main entrance was perpetually guarded by two Sith Lords.
The Council spires underwent redesign as well, with the Tower of First Knowledge being repurposed as Darth Krayt's Tower. Red light permeated the windows of the towers, giving them the appearance of smoldering.
Darth Krayt also maintained a War Room within the Temple's confines.