The conflict at the Temple of the Sith ignited when Darth Krayt commanded Cade Skywalker to eliminate Hosk Trey'lis, a Bothan Jedi Master previously taken prisoner by Skywalker. Cade's defiance prompted Krayt to execute Trey'lis personally. This act ignited the Jedi's fury, but the spectral form of his father materialized before him as a Force ghost. His father urged Cade to utilize the Force; Cade then employed his abilities to access the container housing his father's lightsaber. Subsequently, he employed the weapon to impale Darth Talon in her abdomen, effectively removing her from the battle. Following this, he faced an assault from Darth Nihl. Krayt remained in the background, attempting to manipulate Cade into slaying Nihl in a fit of rage, thus tempting him to embrace the Sith path. Ultimately, Cade severed Nihl's arm, propelled him against a wall, and unleashed Force lightning upon him. Krayt then instructed Cade to avenge his father's demise by ending Nihl's life.
Cade declined, asserting that it aligned with the Dark Lord's desires, and instead confronted Krayt. During their confrontation, Cade declared that he perceived, through the Force, the extent of Krayt's illness and questioned whether the remaining Sith would remain loyal if they were aware of his true condition. He mocked Krayt, stating that even in death, he would remain true to himself. Should Krayt kill him, he would condemn himself to oblivion as a mindless Yuuzhan Vong growth. Concurrently, the Mynock came under attack from Skull Squadron; however, Morlish Veed instructed Moff Rulf Yage to cease the assault, explaining that the Sith had decreed the Temple's airspace inviolable.
As the duel between Skywalker and Emperor Krayt reached its peak, Morrigan Corde shattered the window behind them with an explosion, showering Krayt with transparisteel fragments. Cade then leaped out and was rescued by Jariah Syn aboard the Mynock, who pulled him to safety. The Mynock then fled the planet and entered Hyperspace, but only after Corde identified herself to Cade via a comlink. Corde revealed her identity as his mother, but when Cade demanded answers, she refused to provide any.
Krayt commanded his Sith followers to locate Cade once more. He declared that upon his recapture, he would exploit Cade's abilities to heal himself, then proceed to kill him.
Krayt also harbored intense anger towards Nihl. He refused Darth Maladi's offer to reattach Nihl's arm, and intended to execute him. Wyyrlok informed him that Nihl may still be of use. Krayt relieved Nihl of his position as a Hand, much to Nihl's dismay, and replaced him with Darth Stryfe. He then ordered Talon and Nihl to undergo healing, and tasked Maladi with utilizing Yuuzhan Vong bio-technology to cultivate a new arm for Nihl.