With Separatist forces countering their strategies at every turn, Rex and the clone army turns to a squad of unusual clones – those born with "desirable mutations" – to defend the Republic shipyards at Anaxes.
Anakin Skywalker, Rex, and the Bad Batch travel to Skako Minor in search of a signal they suspect could be connected to a friend they believed to be dead – putting them in the line of enemy fire.
After escaping from Wat Tambor's facility Rex, Anakin, and the Bad Batch must fight their way through a droid army, with the planet's local inhabitants uncertain about the visitors' intentions.
When Echo proposes a plan to infiltrate Admiral Trench's ship over Anaxes and give the Republic a much-needed victory, the Bad Batch questions where the clone's loyalties lie – especially with Mace Windu and Obi-Wan Kenobi being used as bait.
After leaving the Jedi Order Ahsoka Tano crash-lands in the Coruscant underground, where she befriends an ambitious young pilot named Trace – whose sister, Rafa, is in over her head.
Ahsoka strikes a deal with the Pykes to free her friends -- but the Martinez sisters rally and return to try and rescue her. Meanwhile, a discovery inside the facility portends the return of an old foe.
When Ahsoka and Bo-Katan inform the Jedi about Maul's presence on Mandalore, Obi-Wan and Anakin send Rex and a contingent from the 501st under Ahsoka's command to try and capture him.
As Bo-Katan and the clones clash with Saxon's Mandalorian forces, Ahsoka squares off one-on-one against Maul, who taunts her with his knowledge of Darth Sidious' plan to conquer the galaxy.
While en route to Coruscant with Maul as her prisoner, Ahsoka finds herself on the run from Rex and her former friends after Darth Sidious orders the destruction of the Jedi.
With their former friends turned against them, Ahsoka and Rex work together to try and escape the cruiser – as the grand Republic falls to the rise of a new Galactic Empire.
