As the Empire further asserts its control over the galaxy, Imperial systems are becoming more commonplace. Just like on Saleucami in "Cut and Run," the use of chain codes has now been implemented on Ryloth.
The limits of a clone trooper's programming -- and loyalty to the Empire versus the Republic -- is starting to make itself clear in this episode, as we see Captain Howzer lead a small revolt.
In later years, Cham Syndulla makes good on his promise to return to Ryloth in an attempt to free his homeworld. The struggle between Cham's Free Ryloth Movement and the Empire continues in the novel Dark Lords of the Sith and the Star Wars Rebels animated series.
