On Friday, Disney+ debuted the penultimate episode of Star Wars: The Clone Wars, "Shattered." Like the previous two episodes, this episode takes place at the same time as the events of Star Wars: Revenge of the Sith. In "Shattered," The Clone Wars catches up to the moment that Darth Sidious enact Order 66, turning the clone troopers fo the Army of the Grand Republic against the Jedi Knights they've been fighting alongside for years. It's a moment that has loomed over the series from the beginning, knowing that one day the clone troopers fans have grown to know and love would be forced to become pawns in Palpatine's scheme to take over the galaxy.
The moment strikes while Ahsoka Tano and Commander Rex are returning from the Siege of Mandalore with Darth Maul as their prisoner. Rex gets a transmission and takes it with a few other clone troopers. Sidious gives Order 66. At almost the same time, Ahsoka senses Anakin Skywalker's fall to the Dark Side as he kills Mace Windu and pledges himself to Palpatine. She tries to tell Rex that something has happened to Anakin. Rex tries to resist his programming. He manages to tell Ahsoka to find Fives before he opens fire.
Fives was a clone that discovered the truth about the inhibitor chips placed in the brains of the clones, how they could be used to turn the clones against the Jedi, and the first hints of Palpatine's true plans. He tried to bring the information to Red and Anakin, but Palpatine branded him an assassin and had him executed. Luckily for Ahsoka, Rex also filed a report about Fives which she was able to access using Anakin's password. The report tells her everything she needs to know about the inhibitor chips.
Ahsoka teams up with some of the droids aboard the ship to trap Rex and get him to a medical bay. There, they scan his brain and, with the help of Ahsoka's Force abilities, find the inhibitor. The droids perform surgery to remove the inhibitor chip. Rex wakes up just in time to assist Ahsoka in defending their position from the other clones.
This explains how Rex was able to resist Order 66 going forward, and how he and two other clones — Gregor and Wolfe — went on to live in isolation after the fall of the Republic. That is until Ahsoka went looking for them and they all joined Hera Syndulla's rebel cell aboard the Ghost in Star Wars Rebels.
The final episode of Star Wars: The Clone Wars premieres Monday, May 4th — Star Wars Day — on Disney+.