In Star Wars: The Bad Batch‘s season 1 finale, a scene in which a Phase II clone trooper informs Admiral Rampart of the successful demolition of Tipoca City confirms that the clones weren’t fully changed by their inhibitor chips after the execution of Order 66. First introduced in Star Wars: Episode III – Revenge of the Sith as Palpatine’s ultimate plan to eliminate the Jedi, Order 66 is retconned in Star Wars: The Clone Wars when it’s revealed that the clone troopers were brainwashed by inhibitor chips, an implant engineered by the Kaminoans that forced them to comply with Palpatine’s orders and betray their Jedi allies.
The Bad Batch season 1 continues this same trend by introducing a few changes and retcons to Order 66 into Star Wars canon, such as the inhibitor chips’ limitations and the clone troopers’ personal experience under the biochip’s control. As early as episode 1, The Bad Batch suggests that the regular clones undergo severe personality changes once the inhibitor chip is activated, making the clones more ruthless and determined to follow the Empire’s orders. The subplot involving Howzer and the other defector clones in episode 12 revealed that some clones can resist their programming. The temporary activation of Wrecker’s inhibitor chip in episode 7 revealed a disturbing detail: While a clone’s free will is restrained by the biochip, their mind remains active during the execution of Order 66, making the clone aware of their own actions, but powerless to stop themselves. In addition to Wrecker’s experience, one scene in “Kamino Lost” further delves into the clones’ underlying emotional state under the influence of the biochips.
In episode 16, Admiral Rampart asks a clone onboard his Imperial cruiser for a status report on Kamino. “The cities have been destroyed, sir. All Kaminoan facilities have collapsed into the sea,” says the clone. In the scene, the clone trooper hesitates and sounds despondent when relaying the information to Rampart. Since Kamino houses many of the clones’ barracks and is the site where all of the clones were created and trained, it makes sense that the clone would have an emotional response to the demolition of their home. What makes this scene interesting, however, is the fact that this particular clone clearly disapproves of the Empire’s actions and yet he still follows their orders instead of defecting like Captain Howzer. This scene then suggests that, while the inhibitor chip removes their agency, the “regs” still retain their past memories and feelings after the execution of Order 66.
The clone trooper scene therefore introduces a new facet of Order 66 – the early stages of the inhibitor chips’ depletion. When Wrecker and Crosshair’s inhibitor chips were first activated, both of them were unable to express their personal feelings because they were overshadowed by the urge to follow the Empire’s orders. After his chip was deactivated, Wrecker remorsefully confesses to Omega that he was unable to stop himself from attacking her. Only after Crosshair supposedly had his inhibitor chip removed did he express his grief at being abandoned by Clone Force 99 and begin to display more humanity towards his former squad. Unlike Wrecker and Crosshair’s experiences, the clone trooper is able to simultaneously follow the Empire’s orders and vaguely express his true feelings, which suggests that the inhibitor chips’ control must be less effective over time.
The scene featuring the clone trooper in episode 16 could possibly be establishing a civil war within the Empire’s military for Star Wars: The Bad Batch season 2. Since the clone trooper that became emotional at the loss of Kamino was based on Admiral Rampart’s Imperial cruiser, the scene reveals that even clones positioned within close range to the highest ranks of Imperial leadership may not be as heavily influenced by their biochips as they were when Order 66 was first implemented, suggesting that their own personality and feelings will resurface over time. Even if some of the clone troopers were to regain their agency, however, the twist involving Crosshair shows that, depending upon the clone trooper’s personality, some clones may choose to support the Empire’s efforts even without the inhibitor chips’ influence.