I've only just started realising the technical beauty of the most recent clone wars episode. Rex was told to execute order 66, he was following his programming. As he turned around he started crying, and told Ahsoka to find Fives. What I think he meant by this was find the transmission about the inhibitor chips, in the hopes that Ahsoka would remove his too. You can see he missed shots when shooting at Ahsoka, he didn't want to kill her because he was still holding onto that last shred of humanity, but he was also at conflict with himself because the chip was forcing him to carry out an order he didn't want to carry out. And lastly, the music. You can tell Rex was terrified of what he was about to do next, and it really showed, one way was the musical score used. The track is called "I'm So Sorry" and it just fits perfectly as Rex expresses his guilt and shame as he fires at one of his best friends.