Warning! SPOILERS for Star Wars Rebels series finale ahead!
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The Order 66, having removed his inhibitor chip before the order to kill the Jedi was ever given. Rex survives the Clone Wars, living in seclusion on the desert planet Seelos with his fellow clones, Wulffe and Gregor, during the time that the Galactic Republic transforms into the Empire.
In Star Wars Rebels, Ahsoka brings Kanan and Ezra to meet the last surviving clones, after which Rex returns with them to up with Phoenix Squadron, and later, the Rebel Alliance. Rex is shown taking place in several missions while with Phoenix Squadron, and in the Rebels series finale, he fights alongside the Ghost Crew and their allies in a battle that results in Lothal being freed of the Empire's control.
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Rebels ends with the liberation of Lothal, but the series finale goes on to include an epilogue that provides further context for what each of the surviving Ghost Crew do next. In a voice-over given by Sabine, she reaffirms that "Hera fought in the Battle of Endor," a detail already made known thanks to several mentions of Hera's involvement with the Rebellion post-Rebels. But Sabine continues her speech and adds, "as did Commander Rex," seeming to confirm the theory that Rex is, in fact, the same old, bearded rebel who appears in Return of the Jedi.
The theory that Rex was present at the Battle of Endor began when Rex was first reintroduced on Star Wars Rebels with an older appearance and new design. Though only around 30 years old by then, Rex appears older due to his being a clone and their having an accelerated early development. And after concept art of a soldier with an uncanny likeness to Rex in the Rebel Alliance's camo uniform was released online, fans felt the theory was just a foregone conclusion.
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The Rebels writer responsible for first sharing the concept art later rolled back his comments, explaining the image was never meant as confirmation that Rex is the same rebel as seen in the film - a character often referred to as "Nik Sant". And to be fair, Sabine confirming that Rex was present on Endor isn't complete confirmation that Nik Sant is Rex, either; there could very well be two rebel soldiers with bushy, white beards who take part in the Battle of Endor.
But the inclusion of the line in the Rebels finale sure comes across like the writers are finally giving fans the possibility it's true. Regardless of whether or not the character seen in Return of the Jedi actually is Commander Rex, it's now been confirmed he did fight in the Battle of Endor. This means that at least one clone was there to see the Empire defeated, fighting until the very end "for a cause they chose to believe in."
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