Background
During the first year of the Sith Empire War, Jedi General Kyp Tayren saw the increasing threat of Sith on the battlefront and loss of so many Jedi Knights during the early stages of the war as a major problem. Attempting to correct this problem, he partnered with Kaminoan scientists to attempt to create the first (intentional) Force Sensitive Clone Trooper. Choosing CT-583-2005 as a test subject for his abnormalities (unwillingness to follow orders, questioning commands, among other traits the Kaminoans find undesirable in Clone Troopers), Rogue's inhibitor chips was removed (and, unrelatedly, found to be faulty) and a small portion of Tayren's own DNA was injected into him. The operation was a success, and though unable to harness the Force as a Jedi would, Rogue successfully gained the limited precognition of a Jedi. Trained relentlessly and given multiple different advantages, such as vibroblades mounted on the elbows of his armor, meticulously customized armor designed to be lightweight and uninhibiting to his movements while still maintaining some level of protection, and exhaustive training in the martial art of Teras Kasi, Rogue became an inhuman killing machine. However, due to his psychological profile being much different than a standard Clone's and a "Bloodlust" state owing to the rather imperfect nature of his creation as a prototype, he was discharged from the Grand Army of the Republic upon completion of his training. Still, General Tayren found him fascinating, and offered to hire him as a mercenary, where he spent the rest of the war performing key missions behind enemy lines. The new line of Clone Assassins fares much better than he did, but he is still the original, and the most deadly.
Motivation
The destruction of the SithEmpire