The decisive event known as the Mission to Malachor marked the end of the Great Jedi Purge. It transpired during an expedition to the planet Malachor led by Jedi Kanan Jarrus, Ezra Bridger, Ahsoka Tano, and the astromech droid Chopper. Their aim was to uncover knowledge that would aid them in their struggle against the Sith and their Inquisitors. During their endeavor, the Jedi encountered opposition from the Galactic Empire's Inquisitors but found assistance from an unexpected source: Maul, a former Sith Lord. In an alliance, Maul and the Jedi collaborated to secure a Sith holocron and place it within the obelisk of the Malachor Sith Temple.
However, Maul betrayed his allies, blinding Kanan with a lightsaber strike. The situation for the Jedi worsened with the arrival of Darth Vader, the Sith Lord, who sought the temple's secrets for the Emperor. Kanan and Ezra worked together to extract the holocron from the temple's obelisk, triggering an implosion that severely damaged the temple. While the two Jedi, along with Chopper, escaped aboard the Phantom, Ahsoka remained to confront her former master, engaging him in a duel as the temple crumbled around them. With Tano presumed dead, the Imperial Era's Great Jedi Purge reached its conclusion. However, Ahsoka had actually survived the implosion.
Not long after the Battle of Fortress Vader, Darth Vader journeyed through a portal created by Darth Momin with the intention of resurrecting his spouse, Padmé Amidala. While navigating through visions, he witnessed himself and his previous Padawan, the Togruta Ahsoka Tano, meeting within a temple and dueling with their lightsabers. The phrases "it was foretold that you would be here," "I am no Jedi," and "you will die" echoed in his thoughts.
Prior to the mission, the Jedi rebels Kanan Jarrus and Ezra Bridger faced relentless pursuit from the Seventh Sister and the Fifth Brother, rendering it almost impossible for them to assist Phoenix Cell in establishing a base. Seeking guidance, Jarrus and Bridger turned to Tano, who suggested they journey to the Jedi Temple on Lothal to consult with Master Yoda. Although Yoda cautioned Ezra against engaging in conflict with the Galactic Empire, Bridger remained determined to support the Rebellion. Yoda then advised Bridger to locate Malachor, which, after Tano provided clarification, Bridger understood to be a planet. Ages ago, the planet served as the location of a great battle between the Jedi and the Sith, resulting in the destruction of both factions.

Following their assistance to the Phoenix Squadron in establishing Chopper Base on the planet Atollon, Jarrus, Bridger, Tano, and Chopper embarked on a journey to Malachor aboard the Phantom. Despite Rex's offer of assistance, Tano insisted that the mission was exclusively theirs. She asserted that the planet held "forbidden knowledge" that would empower them to defeat the Sith and their Inquisitors.
As the Phantom entered Malachor's atmosphere, Chopper detected a second, unidentified vessel. The Jedi and Tano quickly deduced that they were not the only ones on Malachor. This second visitor was identified as the Eighth Brother, an Inquisitor who was pursuing a "shadow," later revealed to be the former Sith apprentice Maul. While Chopper tracked the second vessel, the Jedi and Tano examined a series of monoliths inscribed with an unfamiliar "ancient tongue."
When Ezra inadvertently touched one of the monoliths, the ground beneath them gave way. The Jedi and Tano soon found themselves in an underground tunnel and observed a large, pyramidal Sith temple in the distance. As they traversed an ancient battlefield strewn with fossilized remains and lightsabers, they were ambushed by the Eighth Brother. During the ensuing conflict, the Inquisitor deployed several S-Mine Detonators, causing the ground beneath Bridger to collapse, separating him from Ahsoka and his master.

While Ahsoka and Kanan pursued the Eighth Brother, Ezra attempted to find a way out of the tunnel. Shortly after, he encountered Maul, who introduced himself as "Old Master." Although Bridger initially distrusted the stranger and suspected him of being a Sith, Maul managed to gain his confidence by claiming that he sought the same knowledge to avenge the crimes the Sith had perpetrated against his late mother and brother. Ezra empathized with Maul's situation due to his own grievances against the Empire for taking away his home and parents.
Together, the two Force-sensitive individuals navigated their way through the Sith temple. Following a challenging trial that involved the use of the Force, Ezra and Maul succeeded in obtaining the Sith holocron. Meanwhile, Kanan and Ahsoka managed to capture the Eighth Brother with Chopper's assistance, who turned the Inquisitor's own TIE Advanced v1 starfighter against him. Kanan and Ahsoka led their captive to the Sith temple, but they were soon ambushed by the Eighth Brother's allies: the Fifth Brother and the Seventh Sister. They engaged the Inquisitors in a lightsaber duel.

At this moment, Maul and Ezra stumbled upon the two opposing groups. Maul utilized his lightsaber to assist Kanan and Ahsoka in driving away the Inquisitors. Despite Kanan and Ahsoka's distrust of Maul due to his past actions, Ezra argued for his trustworthiness, recounting their collaboration in obtaining the Sith holocron. Following a tense exchange, Maul convinced Kanan and Ahsoka to cooperate by emphasizing that the Inquisitors would have alerted Darth Vader to their presence. Maul then persuaded his allies to assist him in his plan to place the holocron within the temple's obelisk, claiming that it would grant them the knowledge to destroy the Sith.
With Maul's stated intention of destroying the Sith, the Jedi and Ahsoka agreed to aid him in his mission. While Ezra was convinced by Maul, Kanan remained suspicious of the former Sith. As the four travelers ascended the obelisk, Kanan seized the opportunity to speak with Ezra privately, warning him that Maul could not be trusted. Ezra, in turn, accused Kanan of hindering his progress and asserted that Maul recognized his potential. During their ascent, the two Jedi were ambushed by the Eighth Brother, who knocked Kanan back and attempted to steal the Sith holocron. Before the Inquisitor could harm Ezra, Maul intervened at a crucial moment and drove him off.

With the Inquisitors in pursuit, Maul convinced the Jedi and Tano to separate. Despite Kanan's objections, Ezra chose to accompany Maul to the summit of the obelisk. During their journey, Maul took the opportunity to sow discord between the Padawan and his master. Shortly after, they were attacked by the Seventh Sister and her ID9 seeker droids. Working together, the Jedi and former Sith managed to eliminate the seeker droids and overpower the Inquisitor. While Maul held the Seventh Sister suspended in mid-air, he urged Ezra to kill her. When Ezra refused, Maul killed the Inquisitor himself and criticized the boy for his hesitation.
Following the defeat of the Seventh Sister, Maul and Ezra proceeded to Kanan and Ahsoka's location to assist them in their battle against the two remaining Inquisitors. However, before they could join the fight, Maul stopped, sensing Darth Vader's approach to the temple. Aware of Vader's imminent arrival, Maul hastily instructed Ezra to continue alone to the top of the obelisk while he went to aid Kanan and Ahsoka, and the young Jedi complied. Arriving at the scene, Maul joined the assault on the Fifth and Eighth Brother. Ahsoka managed to slash the Fifth Brother's lightsaber, causing him to drop it and allowing Maul to kill the Inquisitor with a slash through the torso. Meanwhile, Kanan managed to damage the Eighth Brother's lightsaber. The surviving Brother then attempted to flee using his spinning lightsaber to fly through the air, but the weapon malfunctioned and the Inquisitor plummeted to his death below. Having eliminated the Inquisitors, Maul then turned on his allies.

When Kanan demanded to know Ezra's whereabouts, Maul seized the opportunity to strike the Jedi Knight with his lightsaber, slashing Kanan across the face and blinding him. Before Maul could deliver the final blow, Ahsoka attacked him with her two lightsabers. During the duel, Maul revealed that the temple was a powerful battle station capable of annihilating all life and that he intended to use it to exact revenge on all his enemies. Despite his blindness, Kanan mustered enough strength to don a Jedi Temple Guard's helmet and rejoin the battle. Seeing him, Tano taunted Maul, stating that he would have to defeat Kanan before he could challenge her. After instructing Tano to find Ezra, Kanan prepared to fight Maul, and, despite his inability to see, he sensed Maul's attack and managed to knock him off the edge of the temple. He then contacted Chopper and instructed the astromech droid to bring the Phantom to pick them up.
Meanwhile, Ezra succeeded in placing the holocron within the temple's obelisk. He was immediately greeted by a female entity known as "Presence," who revealed the temple's true purpose. When Ezra expressed revulsion, Presence informed the young Jedi that she would instead share the power with someone more deserving. At that moment, Darth Vader arrived on his TIE Advanced x1 starfighter. The Sith Lord attacked Bridger and swiftly defeated him in combat, destroying Ezra Bridger's lightsaber in the process.
Before Vader could finish off Ezra, Ahsoka arrived and confronted the man who had once been her Jedi mentor. Following a hostile reunion, Tano vowed to avenge Anakin Skywalker by killing Vader, who claimed to have "destroyed" him. While Ahsoka and Vader dueled, Kanan and Chopper arrived on the Phantom. Working together, Ezra and Kanan managed to remove the Sith holocron from the temple's obelisk, causing the battle station to abort its firing mechanism. Unfortunately, this action destabilized the battle station's power systems, and the temple began to collapse.

Vader, after a brief duel, managed to use the Force to push Ahsoka off a cliff. Turning his attention back to retrieving the holocron, he quickly returned to the temple obelisk. As the temple continued to collapse, Ezra and Kanan attempted to make their way back to the Phantom. However, Vader caught up with them before they could board the ship and began pulling both the holocron and the two Jedi toward him with the Force. Fortunately for the two Jedi, Ahsoka had recovered from her fall and ambushed Vader. Her attack caught Vader off guard, and she managed to slice away a significant portion of his mask. This damage also affected Vader's voice modifier, and the revealed portion of his face, combined with the distorted but recognizable voice of Anakin Skywalker, confirmed to Ahsoka that Vader was in fact her former master.
Unable to abandon the man who had once been Anakin, Ahsoka chose to remain behind with Vader. Despite a brief moment of silence, Vader reaffirmed his position and attacked her once more. After Force pushing Bridger away to prevent him from entering the crumbling temple, Tano stayed to fight Vader as the room collapsed around them. Tano eventually targetted the floor to destroy it and send Vader falling down, which Vader took as a chance to strike at Tano while she was open. Suddenly, however, a portal appeared from nowhere, with a hand reaching out from it and pulling Tano away before the blade struck her. Tano vanished from Vader's line of sight before he fell as the floor crumbled away and the Sith temple imploded.

Kanan, Ezra, and Chopper managed to escape and returned to Atollon. The two distraught Jedi and Chopper returned to Chopper Base where they informed the other Spectres and Rex about the loss of Ahsoka. Kanan was compelled to cope with his new blinded state. Meanwhile, Ezra's encounter with Maul on Malachor and the apparent loss of Ahsoka ignited the young Jedi's interest in the dark side of the Force. While in his room, Bridger took the opportunity to open the Sith holocron; a feat that could only be accomplished by someone who had tapped into the dark side. Meanwhile, Maul was able to escape Malachor with goals of continuing his relationship with Bridger. Vader also survived his fall and limped out of the temple.
Tano also survived the duel on Malachor. The hand that reached out to her and saved her from Vader's strike belonged to none other than a future Bridger: in 1 BBY, Bridger accessed the World Between Worlds via a portal located in the Lothal Jedi Temple. Upon entering the realm, Bridger was led to a portal to Malachor in 3 BBY by Morai, a convor with ties to both the Force wielder called the Daughter and Tano. Bridger reached out and saved Tano, who thanked him but realized she would need to return to her own time. After an attack from Darth Sidious, Ahsoka became separated from Ezra and escaped back to Malachor, where she would descend into the ruins of the Sith Temple. After watching Vader limp away, Morai joined her. Tano became lost to the shadows and rubble of the Sith temple. Within, Morai led Tano through a flooded floor to a staircase, which led to another portal for the World Between Worlds. Morai flew out of the temple and was spotted by Vader. Tano's supposed death was considered the last act of the Great Jedi Purge, with Vader believing her dead.
The Mission to Malachor was first depicted in "Twilight of the Apprentice," a one-hour season finale that combined the 19th and 20th episodes of the second season of the Disney XD television series Star Wars Rebels. This mission marked the debut of two new characters: the Eighth Brother (voiced by Robbie Daymond) and Presence (voiced by Nika Futterman, who also voiced Asajj Ventress in The Clone Wars TV series). Additionally, guest actors Sam Witwer and Matt Lanter reprised their roles as Darth Maul and Anakin Skywalker, respectively.
Dave Filoni, the supervising director of both Star Wars: The Clone Wars and Star Wars Rebels, had envisioned the final confrontation between Darth Vader and Ahsoka Tano since creating Ahsoka for The Clone Wars. Over the years, Filoni illustrated the conflict between Tano and Vader with different endings until he proposed a sword fight between them to Lucasfilm Story Group's Kiri Hart, who approved his decision. However, one of the earlier planned endings, according to Filoni during Celebration Europe 2016, had Vader killing Ahsoka but not before she slashes his helmet and sees Anakin Skywalker's scarred visage before expiring.
During the episode's development, Vader was initially intended to engage Maul in a duel before facing Ahsoka, resulting in Maul's death at Vader's hands, as Maul's appearance in Rebels was intended as a one-time event. However, the idea became unmanageable due to the abundance of storylines and the lack of emotional connection between Maul and Vader, leading to Maul's survival until the season three episode "Twin Suns."
The Star Wars Book incorrectly states that the mission occurred in 4 BBY.