Chopper's antics cause Ezra and Zeb to forget to carry out an important repair on the Phantom. Hera and Sabine set out to an abandoned Republic asteroid base to retrieve supplies provided by Fulcrum, an anonymous informant whom Hera has been in contact with. Sabine voices her displeasure towards Hera's secrecy about their mission, feeling as though neither she nor Kanan trust her. Due to the fuel tank leaking on the Phantom, the two are left stranded on the base, which is infested with deadly fyrnocks. The two work together to survive the creatures long enough for the rest of the crew to rescue them aboard the Ghost, allowing Sabine to overcome her trust issues while Hera tells her to have faith in the growing rebellion.

Kanan tries to teach Ezra how to use the Force to make a connection to other living creatures. The rebels destroy the Empire's new prototype TIE fighter during a parade celebrating the 15th anniversary of the Empire's creation. Ezra, who was born on the original Empire day and has turned 15, is preoccupied with his feelings towards his missing parents and opts out of the mission. He soon discovers that his parents' Rodian friend Tseebo is wanted by the Empire, and rejoins his friends to look for him. Tseebo is found hiding in the basement of Ezra's old house, where Ezra reveals his parents were arrested for making anti Empire radio broadcasts, after which Tseebo had gone to work for the Empire. The rebels learn that Tseebo has allowed himself to be implanted with cybernetics so he could steal information that is valuable to the Empire, though the sheer amount of information he uploaded has affected his mind. The Rebels smuggle him off of Lothal aboard the Ghost. During the ensuing chase led by the Inquisitor, Tseebo regains his senses and reveals that he knows what happened to Ezra's parents.

Ezra and Commander Sato are captured when a new Imperial weapon—an experimental Interdictor-class Star Destroyer—generates a gravity well strong enough to pull ships out of hyperspace. Hera sends Kanan, Rex and Chopper to rescue them, using a stolen shuttle, stormtrooper armor, and Rex's knowledge of Imperial codes and protocols to infiltrate the Interdictor, although Kanan's lingering distrust of Rex initially hampers the mission. Ezra and Chopper head to the reactor to sabotage the Interdictor, but Rex is captured as he and Kanan escort Sato and his crew to their shuttle. Kanan heads back to rescue Rex and they deploy an escape pod, as Chopper's sabotage causes the gravity well projectors to overload, pulling the other Imperial cruisers towards the Interdictor and destroying it.

Ahsoka informs Kanan that she's continuing her investigation on the Sith Lord Darth Vader, but finding information on him is difficult. In the meantime, she receives word of two sets of coordinates that cross the Imperial net. She heads to look into one of them while dispatching Kanan, Ezra, Zeb, and Chopper to the other. Ahsoka arrives at her location first, a ransacked passenger ship adrift in space, and finds signs of weapon damage all over. The lone survivor, a grandmother, claims "two redblades" kidnapped her grandchild from her and disappeared. Ahsoka informs the team at their destination on a distant planet that the two Inquisitors are involved. Zeb and Chopper locate the Inquisitors' fighters at the spaceport and reclaim the baby stored in one before destroying them, while Kanan and Ezra find the distressed mother of the second child. Chopper takes the first child to the Phantom shuttle while Zeb encounters the Inquisitors on the street after relieving a fleeing droid of the second baby. Kanan, Zeb, and Ezra discover that the children are force sensitive and were targeted by the Inquisitors to ensure they do not become Jedi. They attempt to lose the Inquisitors through a housing block on their way back to the shuttle, but are overpowered by them. Ahsoka appears and easily defeats both of the Inquisitors while the rest escape, using the Force to jump up and join them in the shuttle as it passes overhead. The Rebels escape, but not before one of Seventh Sister's probe droids hears Ezra saying they're going to the planet Garel.

Ahsoka, Ezra, Kanan and Chopper arrive on Malachor – a Sith world long forbidden to the Jedi – in search of knowledge, discovering a cavern containing a Sith Temple amid the site of an ancient battlefield between Sith and Jedi who used cross guard lightsabers. They soon are attacked by a new Inquisitor, the Eighth Brother, who is hunting a mysterious hermit calling himself "Old Master." When Ezra encounters the hermit, he reveals himself to be Maul (Sam Witwer) and offers to help Ezra get into the Temple, aiding him in recovering a Sith holocron. When the other Inquisitors arrive and alert Darth Vader of their presence, Ezra convinces the group to work together in spite of Kanan's fears that Maul is corrupting his student, allowing them to finally kill the three Inquisitors. However, Maul soon betrays the group and blinds Kanan with his lightsaber, revealing his true intentions of making Ezra his apprentice. Although sightless, Kanan dons the mask of a fallen Jedi Temple Guard and throws Maul from the top of the temple. Ahsoka finally faces Darth Vader – who has cornered Ezra and destroyed his lightsaber – and comes to terms with his identity as Anakin Skywalker as she engages him in a duel, while Kanan and Ezra remove the Sith Holocron. Unable to abandon her old Master, Ahsoka stays within the crumbling temple and stalls Vader while Ezra, Kanan, and Chopper flee the planet and reunite with the Ghost crew. Maul flees Malachor in one of the Inquisitor's ships while Vader, who survived the destruction of the temple, walks away as a convor watches from above and an unknown figure is briefly seen limping into the shadows. As the Ghost crew tries to cope with their losses, Ezra continues to meditate on the Sith Holocron and finally succeeds in opening it.

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, meanwhile, is struggling with his blindness when he discovers Ezra's use of the holocron and confiscates it, before being summoned out into the Atollon wilds by a mysterious call that proves to be from the Bendu (Tom Baker), an ancient Force user who is neither Jedi nor Sith but rather "the one in the middle". 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 Grand Admiral Thrawn (Lars Mikkelsen). The Bendu helps Kanan to realize that the Force grants him abilities that can make up for his lost sight, and on sensing Ezra's peril on the mission Kanan leaves to go help him, leaving the holocron with the Bendu. The Rebels secure a handful of fighters but lose the Phantom after Ezra sets the shipyard plummeting, and it is only the timely arrival of the Ghost and other rebel ships that saves them after Thrawn determines that they are not dealing with the entire rebel fleet and orders his forces to allow their escape. Ezra is suspended, but expresses his gratitude to Kanan for rejoining the action while the rebels learn that the Y-wings are to be delivered to General Dodonna's unit.

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",^[46] had avoided the army-wide shutdown command and now wants to pit his forces against Rex and the Jedi in order to determine whether the Separatist or Republic forces are superior once and for all. As Rex, Ezra, and Kanan battle the droids, Chopper sneaks away and sends 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 Neimoidian shuttles. However, the Empire also receives the distress call and dispatches an assault force. Rex and the Jedi reach "Kalani", and Ezra points out to him that neither the Republic nor the Separatists won the Clone Wars, but were in fact both defeated by the Empire. Ezra also notes that since the Separatists were originally fighting to resist tyranny, the battle droids should naturally oppose the Empire. "Kalani" sees the logic in Ezra's words, with the Ghost crew and the droids working together to escape the Imperial assault force in two of the three vintage Neimoidian shuttles Chopper found; the one on which the Spectres escape replaces the lost Phantom. Calculating that the Rebellion has less than a 1% chance of succeeding against the Empire, "Kalani" amicably parts ways with the Rebels. Rex congratulates Ezra for doing what no Senator, Clone, or Jedi ever could: convincing clones and battle droids to set aside their differences and agree to peace.

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-class Star Destroyers. 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 Konstantine's Interdictor, 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. With the battle going poorly, the Rebels are forced to retreat back to their base on Atollon and activate its shield generator, protecting them from the Imperial fleet's bombardment. Thrawn responds by sending a ground force to assault the base. Ezra reaches Sabine and convinces her and Rau to lead a small Mandalorian force to destroy the remaining Interdictor cruiser, which will allow the Rebels to escape. Thrawn's forces breach the base's defenses, but before he can capture the Rebels, the Bendu intervenes, attacking the Imperial forces and distracting them long enough for the Rebels to evacuate, but attacks them as well. At the same time, Ezra and Sabine destroy the Interdictor. Kallus escapes imprisonment and ejects in an escape pod to be picked up by the Ghost crew. The Rebel fleet then escapes. Back on the surface, Thrawn incapacitates the Bendu, who warns Thrawn that it has already foreseen his defeat. Refusing to believe this, Thrawn attempts to kill the Bendu personally, but it disappears before the shot can hit it. The remaining Rebel fleet leaves to rendezvous with the rest of the Rebellion at Yavin IV, and Hera promises to help Sabine and the Mandalorians on an upcoming mission. Ezra is worried about the massive defeat the Rebellion has suffered, but Kanan points out that it is in fact a victory since they escaped. He then tells Ezra that he foresees a future where everybody is free, but that they will have to fight to make it happen.

Sabine, Kanan and Ezra lead Clan Wren in a raid on a Clan Saxon outpost to rescue Sabine’s father who is being held captive by Clan Saxon on behalf of the Empire. The outpost turns out to be a trap to capture Sabine but they are rescued by Lady Bo-Katan of Clan Kryze. As Bo-Katan should have become ruler of Mandalore after her sister, Duchess Satine, was murdered, Sabine attempts to give her the Darksaber but Bo-Katan refuses to accept it. Sabine’s father is to be moved to the capital city for a public execution, so Sabine plans to rescue him as he is being transported there. They attack the convoy and succeed in rescuing Sabine’s father, Alrich Wren, who turns out to be as much of an artist as Sabine. Sabine is contacted by her mother just as the Empire reveals a new weapon, the sound of which Sabine recognises. They rush to the site of the attack and find every Mandalorian warrior vaporized. Sabine is devastated as she realises they were killed by a weapon she personally designed for the Empire, but is relieved to find her mother and brother have survived the attack. As more Imperials arrive, Sabine and her allies are rescued by Clan Kryze, while Bo-Katan and Ezra destroy the pursuing TIE fighters. Saxon shows a recording of the weapon's field test to Thrawn—the weapon superheats an alloy in Mandalorian armor, killing the occupant, but leaving stormtroopers unharmed. 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. Sabine convinces Clan Kryze to join her in a raid on Saxon's Star Destroyer to destroy the weapon. During the assault, Sabine is incapacitated by Saxon, who orders her to adjust the weapon to its full power. She does so, but she also recalibrates the weapon to target Imperial armor, which stuns the Imperial troops. Sabine slashes the weapon with the Darksaber, breaching its power core and destroying the Star Destroyer. At the Kryze camp, Sabine gives Bo-Katan the Darksaber, making her the true leader of Mandalore.

After the Lothal rebels have taken shelter in the ancient settlement, they discover a Mining Guild ore crawler stripping Lothal's surface for raw materials passing by, and decide to hijack it to establish contact with Hera and the Yavin rebel base with its communicators. However, the crawler's captain shuts down the vehicle and raises the alarm, and as Sabine works to reactivate it, Kanan and Zeb discover a number of slaves in the hull, among them Vizago, who was sold to the Guild by the Empire. Working together, the rebels and the former slaves waylay an incoming Imperial patrol investigating the distress call and prevent the captain from destroying the crawler. In the meantime, Hera, unwilling to wait any longer, inspires rebel command to conduct an immediate assault on the factory where the TIE Defender is being produced, and after communication is established, Ezra's team agrees to coordinate the impending assault from the planet's surface.

Hera and her assault team arrive at Lothal and begin to battle their way past the Imperial blockade, while the Ghost crew on the ground sabotage the anti-aircraft batteries to allow an unhindered attack on the TIE factory at Lothal's capital. However, with Thrawn coordinating the Imperial defenses, the Rebel attack force is annihilated, with only a few survivors – Hera, Chopper and pilot Mart Mattin – managing to reach the surface and regroup safely. As Hera's group attempts to slip out of the city under constant pursuit 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. Hera opens an escape route, but is captured by Rukh before she can use it. Mart and Chopper are then picked up by Kanan and brought to the rebels' hideout as the Loth-Wolf watches.

With Pryce as their prisoner, the Rebels force her to give them the clearance codes to infiltrate the Imperial command center at the capital. They seize the control room and plan to issue an evacuation order for all Imperial forces to return to the command center, then launch it into space to self destruct. Rukh overhears the plan and warns Thrawn, who tasks him with disabling the planetary shield. Kallus issues the evacuation order and all Imperial forces enter the command center, but before they can launch, Thrawn arrives and positions his Star Destroyer directly above the city. Once Rukh disables the shield generators, Thrawn orders the Rebels to surrender or he will bombard the city. Ezra decides to surrender to stall Thrawn while the rest of the Rebels move to reactivate the shields. Thrawn puts Ezra in contact with a hologram of Darth Sidious. Meanwhile, Mart realizes the plan is in trouble, and takes the Ghost to enact a backup plan Ezra had given him by sending a signal over frequency zero to summon help. As the Rebels fight their way to the shield generator, Sidious tries to tempt Ezra with a promise to revive his parents. Ezra refuses the Emperor's deal and escapes custody, while the Rebels are able to raise the shield before Thrawn can commence bombardment of the city. Zeb is able to trap Rukh inside the generator as it activates, killing him. Gregor is mortally wounded in the fight and dies. Ezra fights his way to Thrawn, and reveals that he arranged Mart to call the purrgil, who arrive and destroy Thrawn's fleet. The purrgil then grab Thrawn's flagship and prepare to drag it into hyperspace. Despite pleas from his friends, Ezra decides to stay on the ship to make sure Thrawn is defeated for good, and they jump away. With Thrawn's fleet gone, the Rebels proceed with the plan to launch and destroy the command center. Pryce chooses to stay and go down with it rather than remain a prisoner of the Rebels. Upon witnessing the destruction of the command center, the people of Lothal celebrate, and Hera is confident that they will be able to resist any Imperial attempts to recapture the planet.