Baylan Skoll, a fallen Jedi, and his apprentice Shin Hati assault a New Republic cruiser to free Morgan Elsbeth. Morgan informs them that former Jedi Ahsoka Tano, who apprehended and interrogated Morgan, is searching for a star map that will lead to Thrawn. The last remaining grand admiral of the fallen Galactic Empire, Thrawn has been missing for years since he and rebel hero Ezra Bridger were taken to an unknown location by a pod of purrgil (space whales). Ahsoka fears that Thrawn could return and help rebuild the Empire, but is also hopeful that Ezra can be found alive. She and the ancient Jedi-training droid Huyang obtain the star map based on information from Morgan, but are unable to unlock it. New Republic general Hera Syndulla informs Ahsoka of Morgan's escape and suggests she get help unlocking the map from Sabine Wren, Ahsoka's former Padawan learner.

Baylan and Shin take the map to the planet Seatos. Morgan explains that Thrawn is trapped in another galaxy and the map shows the path to get there, starting from Seatos. While recovering from Shin's attack, Sabine tells Ahsoka about the map but does not know which planet the path to the other galaxy starts on. Ahsoka defeats an assassin droid that Shin left behind on Lothal and Sabine traces its origins to Morgan's factories on Corellia. Ahsoka and Hera travel to the Corellian shipyards where they discover a massive hyperdrive being built by workers loyal to the Empire. As a transport takes off with the hyperdrive, Hera chases after it while Ahsoka duels Marrok, a former Jedi-hunting Imperial Inquisitor who is working with Baylan and Shin.

Sabine restarts her lightsaber training under Ahsoka and Huyang's guidance, but struggles with her inability to use the Force like other Jedi. Hera meets with New Republic chancellor Mon Mothma and several senators and asks them to send additional forces to Seatos. Her request is denied when Senator Hamato Xiono, who does not believe Thrawn and Ezra are alive, accuses Hera of using the threat of Thrawn's return to re-direct resources to a futile search for Ezra. Ahsoka, Sabine, and Huyang arrive at Seatos and discover the Eye of Sion, Morgan's large starship which the hyperdrive is being installed in. Shin and Marrok attack with a squadron of fighters, during which Ahsoka attempts to continue Sabine's lessons. Forced to land on the planet below, they pass through a pod of purrgil, evade the fighters, and hide in a forest. Based on a scan of the Eye of Sion, Huyang determines that the ship can make an unusually fast and long hyperspace jump which would allow Morgan to reach the other galaxy.

Ahsoka, Sabine, and Huyang dispatch Baylan's droids. Fearing that Morgan and Baylan will soon have what they need to jump to the other galaxy, Ahsoka and Sabine head towards Baylan's location. Huyang asks them to stay together, and Ahsoka warns Sabine that they may need to give up the chance to find Ezra if it means preventing Thrawn's return. Confronted by Shin and Marrok, Ahsokahugs Marrok while Sabine fights Shin and encourages Ahsoka to go on alone. Ahsoka engages Baylan and retrieves the map, but drops it when it burns her hand. Shin flees when Sabine gets the upperhand, and Sabine arrives to see Baylan send Ahsoka plummeting into the ocean. Sabine threatens to destroy the map, but hands it over when Baylan promises to reunite her with Ezra. The map's details are uploaded to the Eye of Sion and then Baylan destroys the map.

Anakin tells Ahsoka that she has a chance to survive and he has come to finish her training. He asks her to choose to live, and attacks her. On Seatos, Hera and Huyang search for Ahsoka and Sabine. Hera's son Jacen, who has a connection to the Force like his father Kanan Jarrus, hears the sounds of Ahsoka and Anakin fighting and directs the search party. Ahsoka relives fragments of her youth during the Clone Wars and expresses concerns about her legacy as a soldier and as the student of Anakin, who fell to the dark side and became the Sith lord Darth Vader before being redeemed with his passing. As Anakin continues to fight her, Ahsoka comes to terms with these issues and chooses to live on.

The Eye of Sion arrives at Peridea, the ancient homeworld of Morgan's people—the Nightsister witches—who were the first to harness the purrgil and travel between galaxies. Morgan, Baylan, Shin, and Sabine meet the Great Mothers, three Nightsisters still living on Peridea who are allies of Thrawn and who used their Force magic to call Morgan to them. Baylan reveals to Shin that he is searching for a great power on Peridea that he learned about in Jedi folktales. He hopes to use this to end the cycle of war and destruction between the light and dark sides of the Force, as seen with the fall of the Jedi and rise of the Empire. Thrawn arrives aboard his Star Destroyer, the Chimaera, and honors Baylan's promise by providing Sabine with provisions and a mount to search for Ezra.

At a disciplinary hearing on Coruscant, Senator Xiono requests that Hera be court-martialed for disobeying orders. Senator Leia Organa, an ally to Hera and Ahsoka, sends her protocol droid C-3PO with fake evidence that Hera's actions were a miscommunication; the court absolves Hera. She and Mothma discuss the threat of Thrawn's possible return. Sabine catches Ezra up with what he has missed since disappearing. When the purrgil arrive at Peridea, they enter a minefield left by Thrawn. Ahsoka and Huyang exit their purrgil's mouth before it flees, and hide in a debris field until Ahsoka locates Sabine through the Force. Ezra, Sabine, and the Noti are attacked by Shin, the bandits, and Thrawn's night troopers.

The Chimaera is loaded with a mysterious cargo and docks with the Eye of Sion. Ezra constructs a new lightsaber using spare parts from the saber of Kanan, his master. Huyang tells Ezra that Ahsoka originally stopped training Sabine out of fear for her potential after Sabine's family werehuged during the purge of Mandalore. Ahsoka now says she is committed to Sabine. Ahsoka, Sabine, and Ezra are attacked by Thrawn's night troopers and Morgan. The Great Mothers use magic to resurrect the troopers each time they arehuged. While Ahsoka duels Morgan, Sabine and Ezra reach the Chimaera as it departs.