He continued his research in his new work with the Empire, with the Empire listening intently to his theories all the time which only further stroked his already bulging ego. Morality never entered into K'zzt's mind as only his life's ambitions and serving the Empire mattered to him. This changed, however, when his wife gave birth to K'zzt's first child; a son. K'zzt looked down upon his son in the maternity ward and held his tiny hands, suddenly realizing that what he was doing was wrong; life should not come from clone vats but from nature itself, where the being had the right to make their own decisions instead of having everything decided for them. He decided that life was far too precious to be mass produced.
He soon realized that his own life was not much better than that of the stormtroopers he created; in a way, he was just like them, having been conditioned to be a loyal servant of the Empire with no choices, no objections to the way things were run, and of course no second chances. Looking back, he noticed that whenever he had had second thoughts on what was happening, he would quickly be reminded of his "patriotic duties" or sometimes seduced with trinkets and flattery; two things he would soon learn to do without. He felt deeply ashamed of his life, and so decided to secretly join the Rebel Alliance.
He started to supply the Alliance with a steady stream of information in regards to Imperial genetic engineering projects, as well as stormtrooper programming flaws and tactical subroutines. Occasionally he would also plant subversive subroutines within stormtroopers' minds which caused them to act as spies or one-man suicide bombs without even realizing they were doing so. Unfortunately for K'zzt, this did not last. The Imperial Security Bureau soon became suspicious of him and infiltrated both his personal life, as his wife was in fact an agent working for them, and his workplace with spies and surveillance devices. His wife soon discovered what her husband had been doing and, acting as a good Imperial citizen, turned him in without even having to think about it.
K'zzt learned of this, however, and before the ISB agents could come to take him away he conducted one last act of self-defiance; he sabotaged his entire laboratory's computers and "brain-jacked" himself into one of the clone tanks, having his entire mind transferred into the clone body of Colonel TC-1289. When the security forces arrived to arrest him, they simply discovered his former body, shot dead with a self-inflicted blaster bolt to his head. Though they did notice that there were some wires connecting his head to an undamaged , they dismissed this as a failed attempt at electronic sabotage.
K'zzt lived on in his new body, sharing his mind with that of the mindlessly loyal TC-1289. Though at times he would appear to be nothing more than another drone in the Stormtrooper Corps, at others he would be completely himself and contacted the Rebel Alliance on several occasions giving call signs and signals known only to him. This greatly confused Alliance forces, as they did not know how a stormtrooper would have access to these codes and so Airen Cracken issued a 10,000 credit reward for his capture. Alliance High Command feared that, if left on his own, Imperial security may have grown suspicious of the circumstances of K'zzt's death and reopen his case and, upon hearing the reports of an eccentric stormtrooper colonel, they may do a simple background check and discover that K'zzt was still alive. The Alliance did not give this information to the bounty hunters hired to capture him, however, they simply told them that TC-1289 was a wanted criminal.
By the time of Grand Admiral Thrawn's campaign against the newly formed New Republic, K'zzt was still known to have been in Imperial service in his clone body. His last known location was on board the Star Destroyer Crusader in the Kala sector.