Clone Troopers were the main fighting force of the Galactic Republic and the predecessors of the later Imperial Stormtroopers. They were quickly created in vast numbers to supply the Republic with a full-scale army due to the secession of the Confederacy of Independent Systems - a three year long conflict which, due to their involvement, came to be known as the Clone Wars. They were in spite of themselves partly responsible for the fall of the Republic and responsible for the extinction of the Jedi.
The Clone Troopers were secretly implanted during their creation process with mind-control chips, allowing Palpatine to order the clone troopers to execute their own Jedi commanders. This command, Order 66, was given by Palpatine at the end of the war, right after the Separatists were largely defeated. A few days later Palpatine declared himself Emperor and reformed the Republic into the Galactic Empire.
Although the Order and it's outcomes were known to the Jedi and the Senate, the only way possible for the Troopers to execute that order immediately with no hesitation was if a bio-chip controlled their mind and forced them to do it. Alongside this, the Blockade of Naboo which gave the Chancellor (Palpatine) emergency powers was also necessary to have the authority to give out the Order.
After the end of the war, the clone troopers became the first Imperial Stormtroopers, but as the years passed they were gradually phased out and replaced by naturally-born recruits drawn from across the galaxy. The Emperor declared that the clone troopers had succeeded in winning the war and fulfilled their purpose, and the remaining clones were simply retired.
Afterwards, decomissioned Clone Troopers tried to find a place in the galaxy, and met a wide variety of fates. Many took menial jobs as dock workers or farmers on backwater planets, or various other odd jobs, though a rare few were retained for extended periods of time as long-term instructors at Stormtrooper academies.
In behind the scenes videos, writers Filoni and Hidalgo have repeatedly mentioned that Clone Troopers age about twice as fast as normal humans. Their growth rate was accelerated so that it only took ten years to mature them to battle-ready status (biologically around their mid-20's); they did not, however, start aging more slowly like a non-cloned human after that. In Rebels, only 15 years have passed since the Clone Wars ended, but instead of being physically in their mid-40's, the clones physically look like older men nearly 60 years old (albeit still physically active and fit ones).
- In the Rebels Recon for episode 2.2, Pablo Hidalgo was asked what happened to all of the Clone Troopers after the Clone Wars ended (in the fifteen year gap between the earlier Clone Wars TV series and Rebels), and he stated: "A lot of different things happened to them. Some of them had pretty sad situations. In many ways the Clone Troopers are sort of this 'lost generation' of unappreciated veterans who helped save the galaxy and were then discarded. Others though, stayed loyal to the Empire, and became sort of a training guard - they became the instructors at academies across the galaxy, training the next generation of soldiers" (the non-clone Stormtroopers).
- In "Stealth Strike", Admiral Titus tried to tempt Captain Rex by offering him one of these rare academy training positions.
- In Star Wars Episode VII - The Force Awakens, only one line of dialogue directly references anything from the Prequel Trilogy, and it regards the Clone Troopers: after the First Order's Stormtroopers fail in a mission, the villain Kylo Ren scoffs to their commander General Hux that it might be better if they switched back to using clones.