Mission to Kira Carsen's ship

Centuries prior to his apparent death during the Battle of Zakuul, Tenebrae carved a Sith ritual into the flesh of his original body. The ritual was conditioned to unleash a dark plague if his body and spirit were destroyed and infect and invade the minds of anyone in the vicinity, feeding on their memories of the Emperor to recreate himself.

Shortly after the Meridian Complex assault, the Sith Lord Scourge and the Jedi Knight Kira Carsen revealed to the former Alliance Commander they had destroyed the original body of Tenebrae concurrently with the Commander's last confrontation with him. This act rendered them comatose for nearly a year, but they weren't affected beyond that as they had acted as vessels for Tenebrae's power in the past. They were rescued by Satele Shan and her students who in turn were infected and began slowly merging into a hive mind. Carsen and Scourge then stole a cargo ship and quarantined the Jedi task force on board, sending them on a course through the galaxy away from any civilization.

With Tenebrae threatening to return, the duo tested the Alliance Commander on Mek-Sha to make sure they were rid of Valkorion's hidden influences. Upon confirmation, they contacted the Commander (then the leader of the Republic's Task Force Nova) to inform them of this threat.

With Kira and Scourge having lost the ship, the Commander allowed them to send a search party composed of T7-O1 and his droids.

T7-01 managed to find the cargo ship and sent the coordinates to the trio, but was attacked by mysterious assailants and soon lost contact. The Commander, Scourge, and Carsen later arrived at the ship, immediately being attacked by unidentified individuals in an Imperial transport ship. This led Scourge to believe that the Servants of the Sith Emperor had located their master through the Force. At a control panel, Servant Fifteen and Servant Twenty-two were repairing the systems of the ship and reporting to Servant Four. Lord Scourge, ruled by his new emotions, attacked and killed them in a blind rage, blowing their cover.

After the skirmish, T7-01 came out of hiding and revealed that he had encountered a second vessel with no connection to the Servants. While T7 and Carsen disabled the ship's shields and weapons, the Commander and Scourge investigated and discovered that this vessel was of Zakuul. The Commander promptly ejected the shuttle into space.

Scourge and the Commander were then approached by the Force ghost of Revan, who guided them to the location of Satele Shan. Kira made contact with them and urged them to meet her in the medbay. In the medbay, they found the Servants placing the bodies of Satele and her students in a strange pattern, and encountered the Scion Minazar. Minazar, acting on a prophecy by the late Heskal, came to the ship to resurrect Valkorion, declaring his intentions to preserve Valkorion's last vestige from the Servants' "corruption". Servant Four claimed that the Scions and the rest of Zakuul were merely puppets that never knew the true plan of the Emperor and that the Servants were his followers. Servant Four then killed Minazar and was joined by two more Servants, ready to face down the boarding party.

Defeating the Servants, Kira rushed to Shan and her students. The Commander and Scourge then joined her in meditation to enter Shan's mind.

Having successfully entered Shan's mind, the Commander and Kira Carsen encountered Valkorion, who did not appear to recognize them. Two other figures then emerged, representing Vitiate and Tenebrae, the latter of whom condemned Valkorion for becoming distracted by "mortal concerns". Tenebrae vowed to not make the same mistake. The trinity then separated the Commander from their allies, but they were soon joined by Revan, who assisted the Commander in reaching the center of the mindscape. Confronting the trinity once more, the Commander and Revan were joined by Meetra Surik and Scourge. Tenebrae then lashed out to again separate the Commander from their comrades. The Commander was met by the spirit of Darth Marr, who urged them to avenge him and everyone else who had been killed by the Emperor. The Commander was also joined by Senya Tirall, Arcann, Thexan, and Vaylin who also were trying to stop Valkorion from returning.

The Commander reached the center of the mindscape, a memory of the Jedi Temple on Tython. Within, Tenebrae's trinity encircled Satele Shan and arrogantly declared victory over her. Satele then awoke and mocked Tenebrae for his arrogance. In the ensuing battle, the combined forces of the living and dead who were wronged by the Emperor fought the trinity one by one, withstanding his immense power. Vitiate, Valkorion, and Tenebrae turned to dust and crumbled in a similar fashion to the devastations of Nathema and Ziost.