After Order 66, Captain Rex survived, removed his control chip, faked his death with Ahsoka, then spent years helping other clones, living in seclusion, and eventually fighting for the early Rebel Alliance against the Empire.

What Happened To Rex After Order 66?

Quick Scoop

  • Rex’s inhibitor chip is removed by Ahsoka, freeing him from Order 66.
  • He and Ahsoka fake their deaths and go into hiding after the Venator crash.
  • Rex later works in the shadows to help other clones escape the Empire’s control.
  • He eventually lives in semi-retirement with fellow clones Wolffe and Gregor on the AT‑TE walker on Seelos.
  • The Rebellion tracks him down, and Rex fights with the Rebels through the events of Star Wars Rebels and up to Endor.

Order 66: How Rex Survived

When Palpatine issued Order 66, all clones were compelled by their inhibitor chips to execute the Jedi as traitors to the Republic. Rex initially struggled against the order, hinting that his prior knowledge of Fives’ investigation into “Clone Protocol 66” gave him just enough awareness to resist for a moment.

Ahsoka used that brief window to stun and restrain him, then had medical droids locate and remove the inhibitor chip from his brain. Once the chip was out, Rex regained his free will and turned against the execution order, helping Ahsoka escape the other clones on their Venator cruiser.

“I almost killed my friend because of a command I didn’t choose.” – This is essentially the emotional place canon puts Rex in after his chip is removed.

Faking Their Deaths & Going Into Hiding

To escape Imperial retribution, Ahsoka and Rex staged a crash and left behind graves and armor to make it appear they had died with the rest of the clones. This allowed both of them to disappear from Imperial records and gave Rex the freedom to decide what kind of soldier he wanted to be in the new Empire‑dominated galaxy.

For a time, their paths diverged. Ahsoka went into her own exile under an assumed identity, while Rex quietly moved across the shadows of the new regime.

Rex’s Post–Order 66 Journey (Canon Highlights)

Here’s a timeline-style breakdown of what happened to Rex after Order 66, based on current canon sources:

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Era What Rex Was Doing
Immediately after Order 66 Escapes the Venator crash with Ahsoka, removes his inhibitor chip, and helps fake both their deaths to disappear from Imperial records.
Early Imperial years Operates underground, making contact with other clones freed from their chips and helping form a loose “clone resistance” against the Empire’s treatment of clones.
Clone Underground period Helps establish what’s been described as a “Clone Underground,” giving sympathetic clones a way out of Imperial service and trying to protect his brothers from being discarded or abused.
Years of isolation Rex eventually drops out of active conflict and settles on the planet Seelos, living aboard a modified AT‑TE walker with Wolffe and Gregor, largely hunting for food and staying off the Empire’s radar.
Star Wars Rebels era Rex is found by the Ghost crew (Phoenix Squadron) and recruited into the Rebel cause, where he becomes a veteran adviser and front-line fighter on several missions.
Galactic Civil War Story material and commentary place Rex fighting with the Rebel Alliance up through the Battle of Endor, participating in the final defeat of the Empire.

How Fans Talk About It (Forums & Discussion)

On fan forums and Q&A threads, people often debate the “missing years” between Rex’s escape and his reappearance in Star Wars Rebels. Some highlight how The Bad Batch and other media are gradually filling in the blanks, especially his work helping clones question their programming and find freedom.

You’ll see a few recurring viewpoints:

  • That Rex becoming a kind of underground organizer for clones is a natural evolution of his loyalty to his “brothers,” shifting him from soldier to protector of clones themselves.
  • That his later semi-retirement on Seelos feels like a veteran with PTSD stepping away from endless war, until the Rebellion gives him a cause he can believe in again.
  • That his presence at Endor symbolically closes his arc: a clone grown for the Republic ends up helping destroy the Empire that hijacked his entire generation.

Some speculative discussions also ask if future shows will show more of his Clone Underground activity or his earliest contacts with rebel cells, but that material is not fully detailed in canon yet.

Why Rex’s Post–Order 66 Story Hits So Hard

Rex’s journey after Order 66 is often read as a story about reclaiming identity after systemic control. He begins as a loyal clone officer following orders, then survives a moment when his own mind is turned into a weapon against someone he cares about, and chooses to fight that conditioning.

From there, everything he does—helping other clones, resisting the Empire, and eventually fighting with the Rebels—is about making sure his brothers are remembered as people, not disposable tools. For many fans, that makes his older, grizzled appearance in the Rebellion era feel like the payoff of a long, painful, but ultimately hopeful character arc.

TL;DR: Rex survives Order 66 thanks to Ahsoka removing his chip, vanishes with her by faking their deaths, quietly helps other clones resist the Empire, lives in seclusion with a few brothers, then returns to the fight as a Rebel commander all the way through the fall of the Empire.

Information gathered from public forums or data available on the internet and portrayed here.