Taking the Phantom, Ezra, Kanan, and Ahsoka arrive at Malachor. They come across a huge henge crater with six stone spires circled in the center. The Rebels land the Phantom close to one of the spires. Ahsoka notices ancient writing carved in the stone, and as she tries to read it Ezra suddenly touches it, which causes the ground beneath them to crumble. They fall and find themselves in a huge cave where there exists a Sith Temple.
As the Rebels make their way to the temple, they find themselves surrounded by ruins caused by severe battle damage. They also find old lightsabers and many petrified stone bodies. It looked like the remains of a battlefield. From what Ahsoka can tell, the ancient Jedi Knights attacked the Sith Temple which led to no victory for either side. As they walk on, they are suddenly attacked by an Inquisitor known as the Eighth Brother, resulting in Ezra getting separated by Ahsoka and Kanan. Ezra falls down to another level of the cave and survives. The Inquisitor retreats and Kanan and Ahsoka go after him while Ezra looks for another way to get back to them. Observing his surroundings, Ezra has no clue of which way to go. Just then, he is startled by hooded stranger who appears to been marooned on Malachor for years. Ezra draws his Lightsaber as the stranger approaches him, assuring that he means no harm. Ezra remains cautious, but after the old man promises to help him find his friends and what he seeks he reluctantly allows him to accompany him. Searching together, the two of them start getting to know one another, and both realise they are after the same thing from the Temple, knowledge. Ezra also discovers that this stranger knows a lot about the ways of Dark Side, and was once a Force wielder who lost everything at the hands of the Sith. Ezra understands his feelings, since he lost everything he treasured at the hands of the Empire. He now seeks justice, and the stranger reveals knowledge on how he can accomplish that. According to him, the temple contains all the secrets of the Sith that have been long forgotten for thousands of years. Secrets that could be used to destroy the Sith.
Ezra and his new associate make to a sealed door that leads to their prize. The only way the door can be opened is by two force wielders who embrace the Dark Side. Ezra’s first attempt to open the door fails, but by embracing his ultimate power by the ways of the Dark Side, Ezra and the stranger successfully open the door, which led to a passage. Once on the other side, the stranger reveals himself to be the Emperor’s former apprentice, Maul.
Meanwhile, Kanan and Ahsoka have captured the Eighth Brother, and have reason to believe that he was not after them. The Eight Brother reveals that he is after someone else that he refers to as "The Shadow". They tried to get answers from him to no success. Ezra and Maul meanwhile make to a chamber where they discover a Sith Holocron. Working together Ezra manages to retrieve it, but as a result activates something at the top of the temple. Kanan and Ahsoka notice this, and are suddenly attacked by the Fifth Brother and the Seventh Sister. Kanan and Ahsoka engage the three Inquisitors, and so does Ezra and Maul, who is the Eighth Brother's target. Quickly overpowered by the former Sith Lord and the Jedi, the Inquisitors are forced to retreat. Afterwards, Maul explains to the Rebels that he is searching for the same knowledge that they seek, and insists they join forces if they are to survive. Knowing the Inquisitors will send word to Darth Vader, while Kanan and Ahsoka show little trust towards the former Sith Lord, Ezra is more supportive to Maul’s reasoning. So instead of retreating, Kanan, Ahsoka, Ezra, and Maul head for the temple, despite Kanan and Ahsoka’s reluctance to trust Maul.
Pretty soon, the four reluctant allies reach the Sith temple, and begin to make their way to the top. Suddenly they are again attacked by the Inquisitors, in an attempt to get their hands on the holocron. One by one at the hands of Maul, the Inquisitors are defeated and killed, while Ezra makes his way to the top of the Temple. Then suddenly, and unexpectedly, Maul turns on his associates and blinds Kanan with his lightsaber, stating that he wants Ezra as his apprentice. He also reveals that the Sith temple is actually a battle station which he intends to use to exact his revenge on all his enemies. Meanwhile unaware of the deception, Ezra reaches the top of the temple. Blindly following Maul’s given instructions, he places the holocron inside a device that activates a hidden weapon built into the temple. At this point, Maul sees himself victorious and believes he now had the power and Ezra at his will. Although blind, Kanan re-joins the fight and defeats Maul by sending him off the edge of the temple.
Meanwhile, Ezra discovers Maul's deception and worst of all he is confronted by Darth Vader. Ezra engages the Sith Lord in short fight that ends with his lightsaber being destroyed. Vader prepares to kill him, but is halted by Ahsoka. Vader is delighted to finally meet her, and while not adversaries, he assures her the Emperor will show her mercy if she cooperates in revealing the location of any remaining Jedi Knights. Ahsoka declines, and states that there are no more Jedi. Then, after Vader coldly admits to killing her master, Ahsoka engages the Sith in a lightsaber duel to avenge his death. Ezra meanwhile tries to retrieve the holocron but is unable to. But with Kanan’s help, master and apprentice are able to remove the holocron. But as a result, this causes the temple to collapse. Ezra and Kanan try to escape to the Phantom, but Vader tries to stop them from escaping with the holocron. Ahsoka intervenes and causes damage to his mask, revealing him to be her former master, Anakin Skywalker. Seeing that he really is her former master, Ahsoka refuses to leave him again. For a few moments, Ahsoka's compassion appeared to have reached Vader, but he then shrugged it off. Coldly declaring that she will die, he ignites his lightsaber and the pair resume their battle. As the temple continues to collapse, Ahsoka forces Kanan and Ezra to leave without her. Ezra and Kanan successfully escape just as the temple explodes, but Ezra is left devastated for leaving Ahsoka behind. Leaving Malachor behind them, Ezra and Kanan return to the Rebellion with heavy hearts for everyone. Meanwhile, Maul escapes from Malachor in the Eighth Brother's TIE and Vader has survived the temple’s destruction. Ahsoka’s fate remains unknown and Ezra succeds in opening the Sith Holocron.
- Taylor Gray as Ezra Bridger
- Freddie Prinze, Jr. as Kanan Jarrus
- Dee Bradley Baker as Rex
- Ashley Eckstein as Ahsoka Tano
- James Earl Jones as Darth Vader
- Samuel Witwer as Maul
- Philip Anthony-Rodriguez as Fifth Brother
- Sarah Michelle Gellar as Seventh Sister
- Robbie Daymond as Eighth Brother
- Nika Futterman as Presence
- Matt Lanter as Anakin Skywalker
- Samuel Witwer reprises his role as Maul in this episode, who last appeared on-screen in Star Wars: The Clone Wars.
- This is the only appearence of the Eighth Brother.
- The Fifth Brother and the Seventh Sister are killed off in this episode.
- The petrified bodies that were in the remains of the battlefield on Malachor were inspired by the impression of figures left behind after the devastation of Pompeii.
- In the original script, Maul was originally going to be killed by Darth Vader.
- Maul's Lightsaber is the same as The Grand Inquisitor's, with the disc cut off. The sounds are also the same ones as those heard in the movies, whereas The Grand Inquisitor's lightsaber's sounds were developed specifically for the show.
- Kanan becomes permanently blind in this episode.
- Ahsoka finally learns that Darth Vader is Anakin Skywalker.
- At the conclusion of Vader and Ahsoka's battle, a Convor bird watches Darth Vader limp away. Executive Producer Dave Filoni indicates that Convorees such as the one seen in "The Mystery of Chopper Base" and "Twilight of the Apprentice" have a deep connection to the Force, though he kept secret what it was.
- Nika Futterman, the voice of the Presence, also provided the voice of Asajj Ventress in the show's predecessor.