Now we all know that Captain Rex is coming to Star Wars Rebels thanks to the season 2 trailer first shown at Star Wars Celebration. According to episodes production number his return is for 203 so this most likely mean for the first regular episode of the season this Fall (after the season 2 premiere from this Summer)!
In the Order 66 arc of The Clone Wars The Lost Missions, we learned more about this Order 66 that lead the clones to kill the jedi in Revenge of the Sith. It was an Inhibitor Chip put at the earliest stages of the clones embryos that send them in a “trance” to kill the jedi when someone gives them the Order 66. In this The Clone Wars arc, clone trooper Tup from the 501st Legion executes master jedi Tiplar during the battle of Ringo Vinda, this lead the Republic to send him on Kamino to find the reason of his act, Fives is sent with his brother Tup to make sure everything will be alright. It is discovered that Tup had a tumor in his brain causing the chip to dysfunction, Fives secretly removes his chip too to compare it with Tup’s chip and he discovers that every clones have this chip, the Kaminoans pretend this is for the good of the clones, to be sure they are not too aggressive but Fives realizes this chip is not what the Kaminoans say it is and it is part of a great conspiracy at the highest level of the Republic with Chancellor Palpatine being involved at some level, he will tell all of this to Captain Rex and Anakin Skywalker before dying. Anakin obviously does not believe him as he sees the Chancellor as one of “his best friends.”
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However, Captain Rex seemed to have believed Fives, indeed in he is Star Wars Rebels and he is on the rebels side and not in a “trance” wanting to kill jedi. In one of the scenes of the second season’s trailer, we see a scar on Rex’s head and on Wolffe’s head too, at the same place where Fives and Tup got their chips removed. How Rex got his chip removed would most likely have been told in the series finale of The Clone Wars as the final arc of the series would have told Ahsoka and Rex stories before/during/past ROTS events.
Along with Rex, in the second season of Star Wars Rebels, we see Wolffe and Gregor two other clones, why did he choose them ? Why not some of his legion, the 501st legion ? In The Clone Wars, Gregor was a commando clone, with his fate left unknown on Abafar, a clone that fans immediately loved! Wolffe was Plo Koon’s commander and named after the animal wolves (Dave has a well-known passion for the wolves). On a story point of view, Rex may have decided to go to Abafar after the Order 66 was executed by the clones and found Gregor on this planet. Rex and Wolffe found each other working together during the series a few times, as Wolffe was a commander, Rex may have decided to tell him rather to tell just simple soldiers. These questions will probably be left unknown until the final arc from The Clone Wars is released in some forms (comics, novel or other) unless, we learn a few things from it in Star Wars Rebels season 2. Rex removing his chip and later becoming a rebel is an excellent path for this fan-favorite character, the way his story took in The Clone Wars made him the perfect candidate to be one of the clones removing his chip and avoiding Order 66. Serving under Anakin Skywalker during the war gave him the opportunity to fight differently, to think differently than with other generals as Anakin himself is not the usual kind of jedi general.
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“A plan that costs us men! Not clones, men!” – Rex
“I honor my code, that’s what I believe.” – Rex
“I used to believe that being a good soldier meant doing everything they told you. That’s how they engineered us. But we’re not droids. We’re not programmed. You have to learn to make your own decisions.” – Rex

The Umbara arc, a clone focused arc from season 4 written by Matt Michnovetz, gave us many great Rex quotes showing his integrity, his honor, the fact that he cares for his fellow clone brothers. Serving under Pong Krell during the battle of Umbara was a difficult challenge for Rex but he did what was right for his brothers even if it meant disobeying orders. In the end, Rex could not execute Krell, Dogma did, Rex did not execute Krell because he was weak but because this was a coward act to execute someone when he is unarmed and was exactly becoming like the enemy (Krell attempted to execute Fives and Jesse for treason) – a monster. Rex is a man of honor, of experience and as the series showed us in particular the Umbara arc, he will always do the right thing, this arc was actually a turning point in for him. This battle was a massacre for the clones, a lot died against the Umbarans, a lot died killed by each others when Krell sent the clones killing Umbarans who were supposed to be disguised as clones turned out it was clones, not Umabarans and also a lot died killed by the hands of Krell. Rex witnessed all of this and it changed him, made him questions things as one of his quotes say “We’re not droids. We’re not programmed”, this what he realized, though he was wrong in a way as the Order 66 arc later showed, the clones were programmed with the Inhibitor chip to kill jedi when needed, on the other way he was right as the chip can be removed. The Umbara arc ended with Rex thinking about what the clones will become when the war will be over. We know that the stormtroopers in the Empire era are not clones (even if a few clones stayed to serve the Empire), Rex’s concerns were right. I think the results of this arc for Rex character showed, gave us a clue that in the Empire era, he could be a rebel and with Star Wars Rebels we have the confirmation of this. Another thing, Umbara arc showed us is what state of mind Rex might have been when the clones executed Order 66. In the clones vs clones scene, Rex was heartbroken to see his brothers killing each others so seeing his brothers executing Order 66 at the time of ROTS was probably even more heartbreaking, seeing the people he fought with betraying their generals, betraying everything they fought for, betraying the ideals of the Republic. It is possible that during that time, Rex had to kill clones to escape from this hell, this is probably what the series finale of The Clone Wars would have shown.
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New adventures are coming for the clone fan-favorite Captain Rex this Fall, and it is Matt Michnovetz ( head writer of Star Wars The Clone Wars season 6, and writer of many arcs from the same series – The Citadel arc, The Umbara arc, The Maul arc adapted into the comics Son of Dathomir, The untold Kashyyyk arc (featuring once again the Bad Batch clones), The untold Bounty Hunter arc and now writer for Star Wars Rebels) who wrote Rex return for Star Wars Rebels! According to Brent Friedman (writer for The Clone Wars, who is also now a Star Wars Rebels writer) Rex return is awesome!
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