On orders to hunt down the Rebels, and especially the Jedi among them, Darth Vader begins an oppressive campaign against Lothal's populace in order to find the group. 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. The situation is even more complicated when Minister Maketh Tua, fearing punishment for failing to neutralize the Lothal rebels, tries to defect to them in order to escape Vader, offering to reveal the truth behind why the Emperor wants the planet. Vader, however, uses this to his advantage and orchestrates Tua's hug by shuttle explosion, framing the rebels for the act and turning Lothal's population against them. The Ghost crew tries to flee but are cornered by Vader, who injures Kanan and Sabine and nearly kills Ezra before they finally escape. After being smuggled off-world by Lando Calrissian to escape the Empire, the demoralized crew meet up with Ahsoka's rebel cell, but Vader pursues them and proceeds to wipe out most of the rebel ships, discovering Ahsoka in the process. Ahsoka is horrified to learn that Vader is actually her old Jedi master, Anakin Skywalker. She joins the Ghost crew as they vow to join the wider fight against the Empire. Darth Vader later reports Ahsoka's existence to Emperor Palpatine, who issues Darth Vader new orders to dispatch another one of their Inquisitors to capture the crew of the Ghost.
Having barely escaped total destruction of the rebel cell Phoenix Squadron by Darth Vader, Ahsoka Tano sends the Ghost Crew to locate a former military commander somewhere in the Seelos system who has the knowledge of useful hideouts in the Outer Rim. The crew discover the commander to be former clone trooper Captain Rex, accompanied by Commander Wolffe and clone commando Gregor. Kanan is immediately hostile due to the clones' role in Order 66 although Rex claims they removed their brain chips. Ezra negotiates with Rex for information relating to potential bases. In return Gregor enlists them for a hunt by using Zeb as bait to catch an elusive Joopa. With the hunt successful, Rex holds up his end of the deal but Sabine discovers that Wolffe betrayed the Ghost crew's location to the Empire. A skirmish with an Imperial probe damages the Phantom shuttle, the crew is temporarily stranded with the clones waiting for an Imperial assault.
The Empire tracks the Lothal Rebels to Seelos. Admiral Konstantine and Agent Kallus arrive at the Seelos System to capture the Jedi. Rex gives the Lothal Rebels a datachip containing old Republic bases in the Outer Rim. 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. Agent Kallus commands the clones to hand over the Rebels, but when Rex refuses, Kallus arrives with three AT-ATs. Taking advantage of a sandstorm and the Force, Kanan, Ezra and the clones use their AT-TE's main gun to destroy one of the AT-ATs. Meanwhile, Admiral Konstantine is summoned away by Darth Vader. Instead of meeting him, the admiral meets Fifth Brother, who claims that he will succeed where Kallus and Konstantine have failed. The Lothal Rebels prepare to leave on the Phantom, but Ezra is unwilling to leave Rex and the clones behind. Kanan, Ezra, and Zeb commandeer one of the AT-ATs and turn its weapons on Kallus' AT-AT which Rex destroys with a critical hit. Kallus flees the battle on a speeder. Hera returns to pick up the clones and the Ghost crew. Returning to the Rebel flotilla, the Lothal Rebels and Rex reunite with Ahsoka.
Ezra, Zeb, Sabine, and Chopper head out to an old republic medical base in search of vital medical supplies only to be encountered by the Seventh Sister and the Fifth Brother. The Seventh Sister captures Ezra and interrogates him about the whereabouts of Ashoka Tano while Sabine is also captured by the Fifth Brother. Zeb and Chopper eventually rescue them and they all barely escape the inquisitors and head back to the rebel fleet.
In order to flee the pressure of the responsibility of being a rebel and a Jedi, Ezra goes on a rescue mission together with Chopper after they received a distress call. They are surprised to find out the ship in need belongs to Hondo Ohnaka. Hondo offers Ezra to join him.
Since the rebels are in need of a new ship in order to overcome an Imperial blockade, Hera embarks on a dangerous mission to meet an eccentric starship engineer and manages to gain his trust. But will that be enough to get a ship from him?.
On a mission to escort a courier with secret information vital to the rebel cause to a rendezvous point, Sabine must face off against her old friend and partner.
A new Imperial ship captures Ezra, Commander Sato, and his crew, forcing Kanan and the clone to go undercover as stormtroopers to free the rebels.
The rebels learn that the Inquisitors are seeking out Force-sensitive children, and they work together to protect the young ones from the Inquisitors' pursuit.
As the Empire attacks the rebel fleet on Garel, Kanan, and Ezra return to Lothal and find a former prisoner with knowledge about Ezra's parents.
An aide to Bail Organa arrives at Lothal with ships for the rebel fleet. An Imperial lockdown causes the rebels to try and think of a new plan to steal the vehicles.
Needing some new hyperspace routes because of Imperial pressure, the rebels find a shortcut but have to gain permission to use it.
New hyperspace routes are needed due to Imperial pressure and after the rebels discover a shortcut they must first gain permission to use it.
While on a mission to obtain fuel for the rebel fleet, the crew works to protect space creatures from the Techno Union asteroid mining operation that threatens the creatures' lives.
The rebels contact freedom fighter Cham Syndulla, who needs help to fight off the Imperial bombing attack on his planet. While coordinating a plan to overtake and steal the carrier that houses these Imperial bombers, the rebels discover that Cham may have a plan of his own.
Zeb and Agent Kallus find themselves stranded on an ice planet after a failed Imperial ambush of the rebels. With Kallus injured from the escape pod crash, he and Zeb must work together to survive the harsh conditions.
Kanan, Ezra, and Ahsoka return to the Jedi Temple on Lothal, seeking answers from Yoda about the Inquisitors' ability to continually track the rebels.
After Chopper gets left behind at an Imperial outpost, he makes an unlikely friendship.
Kanan, Ezra, and Ahsoka prepare to depart to unravel Vader's secret, while the rebels find a way to fend off the predatory creatures that occupy the planet.
Having found out some information about the Sith, Kanan, Ezra and Ahsoka battle the Inquisitors with the assistance of a new ally.
After gaining information about the Sith, Kanan, Ezra, and Ahsoka battle the Inquisitors with the help of a new ally, but are over-matched when Vader arrives.