Star Wars: Age of Rebellion
In this Star Wars Universe… Post-Order 66
Several weeks after Order 66 was initiated, many clones started to suffer from PTSD. The trauma of killing those they worked with and protected, or forcing themselves not to act on Order 66, caused many to abandon the Empire or commit suicide.
Many remained with the empire, serving to train and command the newly-formed Stormtrooper regiments.
Only a few years later, no longer confident of the clones dedication and loyalty to the Empire, Emperor Palpatine ordered the imprisonment, and shortly after execution, of all remaining clonetroopers.
Many escaped, but most of the survivors were lower ranking clones, not worthy of hunting down for their no-longer relevant intelligence.