During the Jedi purge that followed the war, Atris forsook the other Jedi, blaming them for their apathy and unwillingness to actively fight the threat posed by the Sith Empire. In 3951 BBY, the Jedi Order was all but wiped out at the disastrous conclave on Katarr, when all life on the planet was destroyed by Darth Nihilus. Still on Telos, Atris decided to bring about the Order's rebirth despite what she had inadvertently done to destroy it by leaking the time and location of the Katarr meeting in a bid to draw out the hidden Sith. As remnants of the Sith Empire continued to prey on Jedi, she gathered several Echani, daughters of the famed General Yusanis and collectively known as the Handmaiden Sisters, at the Academy, demanding an oath from each that they would never be trained in the ways of the Jedi, even if they themselves were sensitive to the Force; Atris then instructed them in vigorous mental exercises that were aimed at teaching them to resist Force-based influences. The Handmaidens were intended to protect the Academy from the influence of the dark side; as part of their service they were ordered to deal with any Jedi who showed signs of falling under its sway, including killing them.
Atris was the only one whom the Handmaidens absolutely trusted; she was, in fact, the only Jedi to reside within the Academy. She never trained any apprentices in the ways of the Force while there, as almost nobody knew of the place's existence. Furthermore, Atris herself had never before taken on a Padawan, as Meetra Surik pointed out to one of the Sisters when she arrived at the Academy. While the surviving members of the Jedi Order knew of the secret training facility, they presumed that Atris had been killed and that the Academy had fallen into disrepair. The only Jedi to ever come to the Academy was Surik herself, and only because she had come to retrieve the Ebon Hawk, which had been stolen by one of the Handmaidens—however, upon securing the vessel, she immediately left Telos and Atris behind. Even when the three surviving Jedi Masters, Kavar, Vrook Lamar and Zez-Kai Ell, learned that Atris was still alive and preparing to restore the Order, the Telosian Academy proved to be of little significance to them or their plans. Instead of resurrecting the Order on Telos, they decided to meet in the rebuilt Jedi Enclave on Dantooine in the hope of fighting the threat of the Sith when it was finally exposed.
Following the incident on Dantooine, Brianna, believing Surik to be dead, took Kreia directly to Atris, knowing that her mistress would execute any Sith. However, Atris's belief in the Jedi Council's decision during the Mandalorian Wars, as well as her belief in the Order itself, had been shaken after she observed Surik's conviction. As Atris sought desperately to understand Surik's motives, which was part of the reason for her keeping of the holocrons, she clung even more desperately to her perfect view of the Jedi. However, in light of Surik's choices, she knew that either she or the Council was wrong. Though she placed Surik in the wrong, it only made her more unsettled, as, inwardly, she respected her choice. She had been slowly corrupted by her collection of Sith holocrons, which she had gathered in hopes of using their teachings to fight the Sith. Instead, the influence of the artifacts proved too strong, and they slowly twisted Atris's thinking, causing her to fall to the dark side. It built up a pressure that finally exploded when Kreia, who had now revealed her true identity as Darth Traya after she had killed the three Council members Zez-Kai Ell, Kavar, and Vrook Lamar when they reconvened on Dantooine, coerced Atris into ceasing her self-denials and accepting her new dark persona.
After being informed by an Onderonian colonel named Tobin of the Jedi academy on Telos, who had been in turn informed by Kreia, Darth Nihilus attacked Telos, believing that he could feed on what Jedi were there. Kreia concluded that since he would find only Atris on the planet, he would destroy her and then die of starvation. Traya was especially proud of this plan because it would eliminate two major threats to the galaxy in one stroke. However, things did not go as planned. The handmaidens confronted Brianna. She learned that Atris had told her sisters that Brianna had fallen to the dark side and joined Surik against Atris's wishes. Brianna could not convince her sisters otherwise, and was forced to fight them.
During the duel, she proved herself to have surpassed her sisters in ability, as she managed to defeat them all without killing them. Shortly thereafter, Atris arrived and attacked Brianna. Though Brianna was initially able to keep the corrupt Jedi Master at bay, she was eventually overwhelmed. Atris began torturing her handmaiden with Force lightning; but, before she could deliver the final blow, Surik arrived and Atris lashed in a duel in the Academy's Council Chambers. Surik, however, spared her life. This action was something Atris believed Meetra Surik would never have done.
However, it eventually led her down the path to redemption; but the Jedi historian had become disillusioned about her intents and agreed to voluntarily leave the Jedi Order for a time, no longer wishing to expose the Jedi to her corrupted influence. She was held captive in her sanctum until judged by Mical and the new Jedi Council. Atris was proven to be wrong in her belief that the Sith would not attack Telos twice. Darth Nihilus arrived with his fleet above Telos in order to feed on the Force energy within the Jedi who he believed dwelled at the Academy.
After the duel, Brianna pledged undying allegiance to Surik, renouncing her title of Last of the Handmaidens, and embracing her true name. Before leaving Telos, Traya manipulated the Sith into attacking Citadel Station, forcing Surik to fight off an assault and help defend the station before she could follow Traya. Brianna aided Surik and the Telos Security Force in fending off the Sith assault on Citadel Station before joining Surik in pursuit of Traya. Surik faced Darth Nihilus aboard his flagship Ravager to keep him from destroying Telos, thus preserving the Academy's structural integrity, which he was doing to fuel his hunger for the Force. With the assistance of Nihilus' former Sith apprentice, Visas Marr, and Mandalore the Preserver, Surik vanquished the Sith Lord.
Surik had learned from Atris that Traya had gone to a secret academy on Malachor V, the site of the final battle of the Mandalorian Wars, and the site where Surik had previously lost her connection to the Force after killing countless combatants on both sides by activating the Mass Shadow Generator superweapon during the battle. On this occasion, the Sith Lord intended to use Malachor V—a site where the Force still echoed from those killed by the Mass Shadow Generator—to create a wound in the Force, which in turn would allow her to carry out her goal of destroying the Force itself. When the group arrived at Malachor V, however, the massive storms surrounding the planet damaged the Ebon Hawk, causing it to crash. In the crash, the members of the group were separated, and Brianna was unable to help Surik, who went on to duel and defeat Traya alone.
Following the dark side the entire game the player executes Atris. If the player follows the dark side most of the game they have the choice to execute Atris themselves or leave her to the mercy of the Sith holocrons.
- Star Wars: Knights of the Old Republic II: The Sith Lords: Prima Official Game Guide
- Knights of the Old Republic Campaign Guide