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 murder 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 Seetos 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 but Ezra negotiates with Rex for information relating to potential bases. In return Gregor enlists them for a hunt by using Zeb as bait. 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.

Ezra and the crew begin to develop friendships with Captain Rex and his colleagues.

Ezra, Sabine, Zeb and Chopper venture to an abandoned medical station to salvage supplies but are interrupted by the arrival of Inquisitors.

Trying to escape the pressure of being a Jedi, Ezra responds to a distress call with Chopper; the ship in distress belongs to Hondo Ohnaka, who has an offer for Ezra.

Hera goes on a dangerous mission to acquire a new ship, the B-Wing, to help break a blockade and turn the tide in a crucial battle against the Empire.

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 is sent to Lothal with ships for the rebel fleet, but an Imperial lockdown forces the rebels to come up with a new plan to steal the vehicles.

In need of new hyperspace routes due to Imperial pressure, the rebels find a shortcut but must first gain permission to use it.

When the crew of the Ghost agrees to help two refugees who are revealed to be surviving Lasat, Zeb must come to terms with his past to help his people reach their new home.

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.

When Chopper gets left behind at an Imperial outpost, he forms an unlikely friendship with an Imperial droid, and discovers a base location for the rebels.

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.

Kanan, Ezra and Ahsoka gain information about the Sith and battle the Inquisitors with the help of a new ally, but when Vader arrives they quickly find themselves overmatched.