Duel in the Telosian Jedi Academy

In the aftermath of the war, during the Jedi purge, Atris distanced herself from her fellow Jedi, holding them accountable for their passivity and reluctance to confront the Sith Empire's menace head-on. By 3951 BBY, the Jedi Order had been decimated at the calamitous conclave that took place on Katarr, an event that saw all life on the planet extinguished by the actions of Darth Nihilus. Remaining on Telos, Atris resolved to orchestrate the Order's resurgence, despite her inadvertent role in its near-destruction through the leaking of the Katarr meeting's details in an attempt to draw out the hidden Sith. As remnants of the Sith Empire persisted in their predation of the Jedi, she assembled several Echani women, daughters of the renowned General Yusanis and collectively referred to as the Handmaiden Sisters, at the Academy. She extracted an oath from each of them, promising to never seek training in the ways of the Jedi, even if they possessed sensitivity to the Force. Atris then subjected them to rigorous mental exercises designed to cultivate resistance against Force-based influences. The Handmaidens were tasked with safeguarding the Academy from the dark side's influence, and their duties included confronting and killing any Jedi exhibiting signs of succumbing to its sway.

Atris held the absolute trust of the Handmaidens; indeed, she was the only Jedi residing within the Academy's confines. She refrained from training any apprentices in the Force's ways during her time there, owing to the facility's obscurity. Furthermore, Atris had never before taken on a Padawan, a point Meetra Surik highlighted to one of the Sisters upon her arrival at the Academy. While the surviving members of the Jedi Order were aware of the secret training facility, they operated under the assumption that Atris had perished and that the Academy had fallen into disrepair. Surik was the sole Jedi to ever visit the Academy, her purpose being to retrieve the Ebon Hawk, which had been pilfered by one of the Handmaidens. However, after securing the vessel, she promptly departed Telos, leaving Atris behind. Even after the three surviving Jedi Masters, Kavar, Vrook Lamar, and Zez-Kai Ell, discovered that Atris was alive and endeavoring to restore the Order, the Telosian Academy held little significance to them or their strategic plans. Instead of reestablishing the Order on Telos, they opted to convene at the rebuilt Jedi Enclave on Dantooine, hoping to confront the Sith threat once it fully emerged.

Following the incident on Dantooine, Brianna, under the impression that Surik had died, escorted Kreia directly to Atris, confident that her mistress would eliminate any Sith. However, Atris's faith in the Jedi Council's decision during the Mandalorian Wars, coupled with her belief in the Order itself, had been undermined by her observation of Surik's conviction. As Atris sought to decipher Surik's motivations, partly evidenced by her collection of holocrons, she clung ever more tightly to her idealized perception of the Jedi. Yet, Surik's choices forced her to confront the possibility that either she or the Council had erred. Though she deemed Surik to be in the wrong, it only deepened her unease, as she harbored a secret respect for her choice. The Sith holocrons she had amassed, intending to harness their teachings to combat the Sith, gradually corrupted her. The artifacts' influence proved overwhelming, subtly warping Atris's thinking and leading her down a path toward the dark side. This culminated in an explosive confrontation when Kreia, having revealed herself as Darth Traya after murdering the three Council members Zez-Kai Ell, Kavar, and Vrook Lamar upon their reconvening on Dantooine, compelled Atris to abandon her self-denial and embrace her newfound dark persona.

After an Onderonian colonel named Tobin informed Darth Nihilus about the Jedi academy on Telos, who had been 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 confrontation, Brianna demonstrated her superior abilities, defeating her sisters without resorting to lethal force. Shortly thereafter, Atris intervened, launching an attack on Brianna. Although Brianna initially managed to hold the corrupted Jedi Master at bay, she eventually succumbed to Atris's superior power. Atris began torturing her handmaiden with Force lightning. However, before Atris could deliver the final blow, Surik arrived, initiating a duel within the Academy's Council Chambers. Ultimately, Surik spared Atris's life, an act that Atris believed Meetra Surik would never have done.

Ultimately, this act paved the way for Atris's redemption. However, 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's belief that the Sith would not target Telos a second time proved to be unfounded. 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 learned from Atris that Traya had retreated to a secret academy located on Malachor V. This was the site of the final battle of the Mandalorian Wars, and the location 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 exploit Malachor V—a place where the Force still resonated with the echoes of those who perished due to the Mass Shadow Generator—to create a wound in the Force. This wound would then enable her to achieve her ultimate goal of annihilating the Force itself. However, upon their arrival at Malachor V, the formidable storms surrounding the planet inflicted damage on the Ebon Hawk, causing it to crash. The crash resulted in the separation of the group members, leaving Brianna unable to assist Surik, who proceeded 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.