In 11 BBY, the cloners of Kamino rebelled against the Galactic Empire by using their cloning technologies to launch a war against the Empire. The Empire retaliated with a massive assault on Tipoca City. Boba Fett, with his extensive knowledge of the complex, led the 501st Legion into the corridors of the cloning complex to disable the cloning technology. As the remaining resistance attempted to flee, two of their LAAT/i evacuation transports were shot out of the air.
This uprising provoked Palpatine, who had now made himself Emperor, to decide that an army of genetically identical clones presented too many possibilities of turning against him, just as they had done to the Jedi. Thus, it was through this radical reform that the Fett clones would gradually become overshadowed under a pool of clones from different genetic templates and many more birth-born recruits. Although the Jango Fett template would still certainly be used to produce more clone stormtroopers, the Fett clones would rapidly become lost under the number of recruits, conscripts, and different genetic template-based clones. For all of their loyalty to the Republic/Empire and their unrivaled fighting skills, the Fett clones were "rewarded with the chance" to fight alongside "inferior" and far less skilled soldiers. None of the Fett clones, especially those belonging to the "Fett-pure" 501st would ever truly grow used to fighting alongside the non-Fett stormtroopers that they dubbed as the "new guys".