Ezra, Sabine, Zeb, Chopper and Hera sets out to rescue Hondo Ohnaka, while Kanan finds an ancient force creature know as The Bendu.
Six months after the events of the previous season, Ezra leads a mission to rescue Hondo Ohnaka from an imperial prison, wielding a new lightsaber and displaying Force skills that he's learned from the Sith Holocron in the process. Hondo's intel regards a squadron of Y-Wings due to be destroyed at an Imperial shipyard that the Rebels set out to appropriate, with Ezra being given command of the mission.
Kanan Jarrus, Ezra Bridger, and some rebel soldiers are about to dock on to another rebel cruiser. That cruiser is seen to be damaged so they board to investigate. There is a soldier laying on the ground who claims that a “red blade” cut him and was forced to give up the Ghost crew's location. They contact Hera only to find out that Maul has already captured them. Kanan and Ezra agree to give Maul both the Sith and Jedi Holocrons.
The Rebellion begins suffering heavy casualties due to Imperial ambushes on their convoys, and they risk running out of pilots. Fortunately, they receive a tip from a new “Fulcrum” that several Imperial cadets at Skystrike Academy are willing to defect. Sabine is selected to infiltrate the academy and she meets and befriends a fellow cadet named Wedge Antilles (Nathan Kress). Ezra and Kanan wait in space with a transport ready to evacuate Sabine once she finds the defectors. Meanwhile, Governor Pryce and Agent Kallus arrive at the academy to root out the defectors. Sabine figures out Wedge is one of the defectors, and assures him that she will get him and his friends Hobbie and Rake to the Rebellion.
The Ghost crew makes a supply run to the Twi'lek resistance on Ryloth, only to find out from Cham that under Thrawn's leadership, the Imperials have begun to seize the upper hand, and have captured their home and converted it into their headquarters. This also means that their “kalikori”, an important family heirloom, is in Imperial hands as well. Determined to retrieve her kalikori, Hera decides to return to her home and infiltrate the Imperial headquarters.
On a salvage mission to an old Clone Wars battlefield led by Captain Rex, the Ghost crew is captured by a unit of old battle droids. Their commander, a Super Tactical Droid named “General Kalani”, managed to avoid the army-wide shutdown command and wants to pit his forces against Rex and the Jedi in order to conclude whether the Separatist or Republic forces are superior once and for all. As Rex, Ezra, and Kanan battle the droids, Chopper manages to sneak away and send a distress signal to Hera and Sabine - Ezra then discovers Chopper immediately afterwards, with Chopper also having discovered a trio of intact and still-spaceworthy Nemoidian shuttles.
Sabine continues to try to convince Fenn Rau to have his Protectors formally join the Rebellion, but Fenn remains staunchly loyal to Mandalore. When contact with the Protectors is lost, Sabine, Ezra, and Chopper are sent with Fenn to investigate. However, when they arrive, they find the Protectors base completely destroyed. After they destroy an Imperial probe droid, a squad of Imperial Mandalorians led by Gar Saxon arrive to investigate.
The Ghost crew arrives at a planet to help evacuate anti-Imperial dissidents. They are assisted by another armed freighter that identifies itself as Iron Squadron. Commander Sato explains that Iron Squadron used to be led by his brother, but he was killed in combat, leaving the squadron under the leadership of his headstrong nephew Mart (Zachary Gordon). While the rest of the crew evacuates the dissidents, Ezra and Sabine board Iron Squadron's ship and meet Mart and his crew.
The Rebels form an uneasy alliance with Hondo in order to break into an abandoned Imperial ship to steal its valuable cargo, with Hondo promising them a shipment of proton bombs in return. However, the cargo ship is dangerously close to a heavy storm, making any salvage attempt hazardous. They enlist the aid of AP-5, but Kanan and Hera are worried that Ezra puts too much trust in Hondo. The group manages to board the ship and finds the cargo they are looking for.
Ezra and Kanan return to Lothal to scout the Imperial factory there, intending to destroy it. 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. However, Thrawn is also present in the factory and locks it down, suspecting rebel spies are sabotaging the vehicles being made there. Ezra, Kanan, and Chopper manage to steal the weapon data, and are assisted by Kallus, who reveals that he is Fulcrum.
Ezra is plagued by visions of Maul, who approaches him and Kanan as they consult the Bendu, offering a deal. 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. 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. As the ritual completes, Ezra and Maul are attacked by the spirits of the Nightsister clan.
After the legendary Saw Gerrera (Forest Whitaker) and his rebel squad go missing on Geonosis, the Ghost crew is sent to investigate. Ezra, Kanan, Rex, and Chopper split off to search for Saw while Hera, Sabine, and Zeb stay behind to salvage a still operational shield generator. Ezra and his group are rescued from a battle droid ambush by Saw, who explains that the droids killed the rest of his team, and that they were rebuilt by a Geonosian survivor. Ezra, Saw, and the rest of the group pursue the Geonosian and it activates more battle droids which attack Sabine and Zeb.
Saw then begins to interrogate the Geonosian, demanding that it tell him what the Empire was building on Geonosis In response to Saw's questions, the Geonosian (nicknamed “Klik-Klak”) draws two circles in the dirt. Not understanding what Klik-Klak is trying to say, Saw handcuffs Klik-Klak and forces him to lead them deeper into the ruins. Ezra becomes concerned at the hostility Saw is showing to Klik-Klak, and Rex explains that Saw's sister was killed by a Geonosian-built gunship during the Clone Wars. Meanwhile, an Imperial patrol detects life signs on Geonosis and sends scouts to investigate. Underground, Klik-Klak leads the Rebels to his hideout, where he was protecting a Geonosian Queen egg.
While the rest of the Ghost's crew and Phoenix Squadron are away on an exercise mission, Zeb is left in charge of security at Chopper Base. At the same time, the Empire launches a large number of disguised infiltrator droids throughout the galaxy, and one of these units lands near Chopper Base. Damaged by the Krykna spiders and losing its memory, it is taken in by Zeb, Chopper and AP-5; but after a warning from Agent Kallus about the nature of their foundling, Zeb tries to apprehend it.
Upon being told by Fenn Rau what status the Darksaber Sabine recovered from Dathomir holds among the Mandalorians – especially the prestigious House Vizsla, who once ruled Mandalore – Kanan decides that Sabine should wield it in order to rally the Mandalorians into the ranks of the Rebel Alliance. 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.
Sabine, Ezra, Kanan and Rau travel from Atollon to Krownest in the Mandalore sector in order to straighten out matters with Sabine's estranged family. However, the initial reception is quite hostile, since Sabine is still considered a traitor to her family due to her defection from the Empire. Upon being presented with the Darksaber, Sabine's mother, Countess Ursa, allows her daughter the benefit of a personal conversation, but is still too fearful of an Imperial reprisal against her people, and her husband held hostage, to join with the Rebellion, and so she decides to sell out the Jedi to Gar Saxon in exchange for Sabine's freedom.
An Imperial light cruiser over Lothal intercepts a shuttle fleeing the planet. On board are Ezra Bridger (disguised as a bounty hunter) and the droids Chopper and AP-5. Ezra tells Agent Kallus that the Rebels believe the Empire has intercepted his last transmission as Fulcrum, and they have come to help him defect if his cover is blown. Grand Admiral Thrawn arrives in his Star Destroyer Chimaera, and informs the officers on board that he has asked Colonel Yularen of the ISB to locate the Rebel spy in their midst.
The crew of the Ghost waits in a junk field to rendezvous with and refuel a Rebel ship carrying a secret cargo. The Ghost is found by an Imperial infiltrator probe droid, which the crew manages to destroy, but not before it transmits their location to the Empire. The Rebel ship arrives, and the “cargo” is revealed to be Senator Mon Mothma, who is on the run after recently speaking out against the Emperor in the Senate.
Chopper, AP-5, and Wedge are sent on a mission to an Imperial facility to steal access codes for the factory on Lothal. AP-5 manages to successfully locate and steal the codes. Meanwhile, Chopper accesses the Imperial network and draws the attention of the Controller, an Imperial agent who controls an advanced spy ship. Using his ship's capabilities, the Controller remotely seizes control of Chopper, intending to use him to locate the Rebel base. With their mission successful, Chopper, AP-5, and Wedge head back to rendezvous with the Ghost. AP-5 begins to suspect something is wrong when Chopper acts uncharacteristically nice.
After receiving a holocron message, Ezra tells the Ghost crew that they must go to Tatooine to save Obi-Wan Kenobi from Maul. The crew refuses, as they believe that Kenobi is dead and the message is a trap set by Maul. Ezra and Chopper sneak away and head to Tatooine, but things go wrong as their ship is destroyed by Tusken Raiders. Guided by the holocron, Ezra and Chopper set off across the desert in search for Kenobi. After several hours of aimless wandering, Chopper runs out of power and shuts down. Ezra is then haunted by visions of Maul, telling him that he failed his loved ones. Shortly afterwards, Ezra passes out.
Various Rebel cells begin gathering at Atollon to prepare for the attack on Lothal. However, Thrawn is aware of the Rebel plans and tells Governor Pryce and Grand Moff Tarkin that “The real performance is about to begin” and he has already planned a trap for them. Kallus tries to warn the Rebels, but is captured by Thrawn. Thrawn traces Kallus's transmission and determines the Rebel base's location at Atollon.
Thrawn sends his fleet to Atollon, which includes two Interdictor Cruisers. With the Interdictors in orbit, it is impossible for the Rebel ships to escape and the fleet is forced to fight a losing battle against the Imperials. Knowing that their only chance is to send someone out to summon the rest of the Rebel fleet, Commander Sato sacrifices himself by crashing his carrier into one of the Interdictors, giving Ezra a window to escape. On Atollon, Kanan attempts to ask the Bendu for help, but the Bendu is reluctant due to its neutral role. Kanan then accuses the Bendu of being a coward, which angers the Bendu and it disappears. In hyperspace, Ezra contacts Mon Mothma for help, but she is unable to send reinforcements due to fear of them getting caught in another of Thrawn's traps. With no options left, Ezra decides to ask Sabine for help.