Meanwhile, Thrawn observes the entire event, and impressed with Hera's ingenuity, decides to let the rebels escape. Thanks to his training Ezra quickly proves the most capable student in the class. The rebels discover an underground transmission reporting that Jedi Master has survived and is being held in a high-security Imperial prison on Stygeon Prime. The group manages to board the ship and finds the cargo they are looking for. Kallus secretly provides assistance to Sabine in order to repay his debt to Zeb. As the ritual completes, Ezra and Maul are attacked by the spirits of the Nightsister clan. After they destroy an Imperial probe droid, a squad of Imperial Mandalorians led by Gar Saxon arrive to investigate.
He calls Two-Tubes to pick him up, and Ezra and Sabine are rescued by the Ghost crew after destroying a massive Star Destroyer. Humiliated, Azmorigan and his henchmen intercept the rebels on Lothal to take revenge. Ezra and Chopper head to the reactor to sabotage the cruiser, but Rex is captured as he and Kanan escort Sato and his crew to their shuttle. Ezra, Kanan, and Ahsoka decide to head for Malachor to find a way to deal with the Inquisitors. With the help of a local resistance cell led by Azadi, they manage to infiltrate the factory disguised as workers in order to gain intelligence on a new weapon the Empire is developing. During her vision, Ahsoka faces her guilt over not being present during the fall of the Jedi, while also accepting the fact that her former master, Anakin Skywalker, has become the Sith Lord Darth Vader. The Bendu firsts tests Kanan and Ezra by having them navigate a cave, infested with Atollon's native krykna hexapod spiders.
Hera is then tasked go to a planet whose atmosphere is very difficult to fly in to get a ship being built by a Mon Calamari named Quarrie that can break the blockade. Maul and Ezra arrive on Dathomir, where they use dark magic to complete their holocron vision—a desert planet with two suns, where what they both seek is located. Meanwhile, Governor Pryce decides that the growing rebel threat requires a greater response and requisitions the Seventh Fleet, which is revealed to be under the leadership of the recently promoted. Ezra, Kanan, and Chopper manage to steal the weapon data, and are assisted by Kallus, who reveals that he is Fulcrum. Sabine rescues Ezra and Chopper, but Fenn seemingly betrays them when he takes their shuttle and escapes without them.
Saw decides to give the Geonosians a second chance at survival and lets Klik-Klak go. The two find that the market's sole supply of meilooruns has been purchased by the Empire. Kanan and Sabine return to Concord Dawn, with Kanan still wanting to negotiate with the Protectors and Sabine wanting to get revenge for Hera. Back on Lothal, Ezra receives a vision that Thrawn is returning from Coruscant, meaning that they must enact their plan to seize the capital right away. While saddened at his parents' deaths, Ezra takes solace in that they heard his message, and Kanan comforts him by telling him that his parents live on inside him.
The purrgil then grab Thrawn's flagship and prepare to drag it into hyperspace. Ezra and Kanan wait in space with a transport ready to evacuate Sabine once she finds the defectors. By intepreting an unearthed mural depicting the , Ezra uses the Force to bring the images to life, which show him the location of the door. Ahsoka informs the team at their destination on a distant planet that the two Inquisitors are involved. Meanwhile, Governor Pryce and Agent Kallus arrive at the academy to root out the defectors. Sabine, who resents her family, reluctantly agrees to the proposal and retreats with Kanan and Ezra to the Bendu's abode to be trained in the saber's use, but her persisting frustration at the expectations thrust upon her starts to gnaw on Kanan's own patience. In order to pull the mission off, the Ghost crew contacts Hera's father, the famed Twi'lek resistance fighter Cham Syndulla.
Ezra and Chopper decide to see what has happened. The Ghost crew starts working with the wider Rebel cells, but are divided between joining the larger network and waging open war on the Empire, or staying out of a large-scale fight. Ezra fights his way to Thrawn, and reveals that he arranged Mart to call the , who arrive and destroy Thrawn's fleet. Kallus wishes to take his chances and wait for Imperial rescue rather than be a Rebel prisoner, and both he and Zeb part ways with a newfound respect for each other. To Ezra's dismay, Trayvis reveals himself to be an Imperial spy who has used his anti-Imperial transmissions to identify rebel sympathizers, and claims that Ezra's parents are dead and gone. Kanan manages to interrupt the process. Ezra and the Ghost crew depart for Lothal, using Vizago to smuggle them in because the Empire has severely tightened its grip around the planet and nearly crushed the local rebel cell.
At Bo-Katan's camp, her men confront Sabine for her role in the creation of the weapon which she named the Duchess, after Bo-Katan's sister, Satine. Ezra tries to persuade the clones to join the Rebellion, but Rex and the clones instead offer to delay the Empire so the Lothal Rebels can escape. Kallus swaps his code cylinder with that of Lieutenant Lyste, and uses Lyste's credentials to free Ezra and infiltrate Thrawn's office, where the droids erase Atollon from Thrawn's database and transmit clearance codes for Kanan and Rex to rescue them. Maul threatens to reveal Chopper Base to the Empire unless Ezra accompanies him to complete a ritual in order to reveal to both of them the information they sought from the Jedi and Sith holocrons. She and Ezra sneak into the base while the rest of the crew and Cham distract the Imperial patrols.
Returning to the Rebel flotilla, the Lothal Rebels and Rex reunite with Ahsoka. As Hera's group attempts to slip out of the city under constant assailing by Rukh, Kanan returns to the capital to look for her, only to be stopped by the Loth-Wolf, and he asks it what he should do. The Rebels think they have the element of surprise, but they do not take into account the arrival of Tarkin, who has deduced where they will strike. However, the Imperials send an attack force after the Ghost, forcing it to flee deep underground. However, they are young and inexperienced, and their hyperspace drive is inoperable. After dropping off Chava and Gron, Zeb decides to stay on the Ghost in order to find more Lasat survivors to guide back to Lira San. After several hours of aimless wandering, Chopper runs out of power and shuts down.