Did The Clone Troopers Ever Regret Killing The Jedi?

When I was a kid, I didn’t think twice about the clones obeying orders — they were soldiers, after all. But as I got older and rewatched The Clone Wars and Rebels, the tragedy behind their actions started to hit me. Could they have known what they were doing? That question kept pulling me deeper into their story.

Regret Is Real in Canon

Some clones clearly show guilt, trauma, or remorse after Order 66. In Star Wars Rebels, Rex, Wolffe, and Gregor explain that they removed their inhibitor chips, but you can still see how much the past weighs on them. Wolffe, for example, is paranoid and defensive when he meets the Ghost crew, then slowly comes around and joins their fight. That shift shows someone struggling with what he did.

Rex’s story in The Clone Wars Season 7 adds another layer. Once his chip is removed, he breaks down after nearly killing Ahsoka, then risks his life to save her from the other clones. That’s not just loyalty — it’s someone trying to make up for actions he never truly chose.

Even Commander Cody’s short arc in The Bad Batch points to regret. After saying, “We make our own decisions. Our own choices. And we have to live with them too,” he disappears from Imperial service. His words and actions suggest he’s no longer comfortable following orders blindly.

When clones regain their free will, signs of regret and doubt start to surface. One of the clearest examples comes from the Kanan comic series. In Kanan comic issue 5, Clone Commander Grey, who served under Jedi Master Depa Billaba, later reflects on his actions during Order 66 and says he followed the command “as if under some kind of spell… as if I had no will of my own, no memories of the battles we had fought together.” This shows that he recognized the influence of the inhibitor chip and how it overrode his loyalty and memories.

While Grey never explicitly says he “deeply regrets” killing Billaba, his behavior after Order 66 speaks volumes. Once he becomes aware of what happened, he actively resists continuing the mission. In the comic’s later issues, Grey disables his ship’s weapons to prevent further bloodshed and helps Jedi Padawan Caleb Dume (later known as Kanan Jarrus) escape.

You also see physical evidence of this in Rebels. The older clones have scars where the chips were removed, confirming their stories and showing that they’ve tried to reclaim control over their actions.

Not Every Clone Felt the Same Way

Clones didn’t all react alike once the order was carried out. Some deserted or questioned their role, like Cody. Others, like Crosshair in The Bad Batch, stayed loyal and believed they were doing the right thing. Many never had a chance to feel anything at all because the chips overrode their judgment completely.

This mix of reactions also shows up in older stories. In the 2005 Battlefront II campaign (which is part of Legends now), the 501st narrator speaks about Jedi like Aayla Secura with respect and sadness, even saying they couldn’t look her in the face. The description of their silent march into the Jedi Temple captures a sense of doubt, even if they didn’t talk about it openly.