The Cuis clones represented a group of six prototype clone stormtroopers, developed using the genetic makeup of Sa Cuis, a Dark Jedi who served as one of Emperor Palpatine's personal assassins. Because of their origin, they possessed a significant connection to the Force, setting them apart from the standard soldiers within the Stormtrooper Corps, who were cloned from ordinary Human templates at that point. The Emperor and his apprentice, the Sith Lord Darth Vader, closely oversaw their creation and training as part of an experiment aimed at forming a battalion of obedient clone soldiers versed in the ways of the dark side of the Force. Beyond his Force connection, Vader selected Cuis as a template due to his strong sense of loyalty—a characteristic that the Dark Lord hoped the clones would inherit from the dead Dark Jedi.
In the months that followed Emperor Palpatine's establishment of the New Order in 19 BBY, the Sith Lord Darth Vader gave permission for an experiment to clone the DNA of a Force-sensitive individual. Instead of using the Kaminoan methods employed to create the Republic Grand Army, the Dark Lord of the Sith assigned the project to the Clone Masters at Arkanian Microtechnologies, a company known for using Spaarti cloning cylinders. The source of the genome was the Dark Jedi Sa Cuis, an Emperor's Hand who had tried to kill Vader—as part of the Sith Lord's training—under Palpatine's orders. Impressed by the Hand's combat prowess and Force abilities, Vader captured Cuis after defeating him in battle. Once his Arkanian scientists had gathered enough genetic material from Cuis for replication, Vader beheaded his captive.
Before his demise, Cuis refused to admit that the person who ordered Vader's assassination was Vader's own master, even though Vader had already figured out that Palpatine had sent Cuis to test him as part of his training. Rather than being annoyed by Cuis's lack of cooperation, Vader admired his strong sense of duty as an Emperor's Hand, which Cuis was unwilling to compromise even with the promise of being spared from execution. He hoped that the clones of Sa Cuis would not only inherit their originator's connection to the Force, but also his other qualities, such as loyalty and courage.
After Arkanian Microtechnologies spent over a year replicating the Cuis genome, they produced six prototype clones of Sa Cuis, fully grown and trained as Imperial stormtroopers. While they wore the same standard armor as the clone infantry units in the Stormtrooper Corps, the Cuis clones were equipped with a red lightsaber instead of the E-11 blaster rifle. In addition to their melee combat skills, the clones also learned to use their inherited Force abilities, which allowed them to use telekinetic techniques. After reaching the end of their maturation phase, the Cuis clones were trained at an Imperial training center on the planet Yinchorr. Emperor Palpatine and Darth Vader closely monitored the development of the Cuis clones, but most of their practical instruction was given by another Hand named Sheyvan.
The two Sith Lords personally supervised the Cuis clones during the final stage of their trials. They demonstrated their lightsaber skills against each other and Darth Vader, while the Emperor watched their performance. The last test in their training involved each of the six Cuis clones fighting a clone of Lieutenant Erv Lekauf, one of Vader's most trusted officers. The Cuis clones were disarmed of their lightsabers since the exercise was meant to be non-lethal, but they quickly showed that their Force abilities were enough to defeat clones of an ordinary template. The Emperor was pleased with the results of his new Force-sensitive stormtroopers and told Vader to order an entire battalion of Cuis clones from the Arkanians. As the Sith Lords left Yinchorr for Imperial Center, the Cuis clones joined them as the newest members of Darth Vader's 501st Legion.
While Palpatine and Darth Vader discussed the benefits of cloning an entire army from the Cuis template on their way back to the Imperial capital, Sheyvan rebelled against the Emperor, revealing the treacherous intentions he had held since he discovered Palpatine's other Hand, Sa Cuis. After realizing that he was not the only Dark Jedi assassin working for the Emperor, as he had been led to believe, Sheyvan felt betrayed. During his time as the Cuis clones' personal trainer, the Hand secretly won their loyalty, ensuring that they would fight for him rather than for the two Sith Lords who had only ordered their creation.
Their rebellion surprised the Imperials greatly. With the exception of the Emperor, who Vader noticed was suspiciously calm, everyone aboard Palpatine's Lambda-class T-4a shuttle was caught off guard and unable to stop the Cuis clones from taking control of much of the ship. However, despite their demonstrated superior skills against non-Force-users, both during training and Sheyvan's rebellion, none of the Cuis clones could defeat Vader in combat. The Dark Lord, with the help of Lekauf's clone stormtroopers, fought the ex-Hand and Cuis's clones. The Lekauf clones used flamethrowers to burn four Cuis clones, and Vader Force choked the remaining two. Sheyvan fought Vader alone in a short duel, but was killed when he was cut in half from shoulder to hip. Afterward, Vader and Palpatine had the Sa Cuis template decommissioned, though the latter remained open to the idea of cloning a Force-sensitive army in the future.
Because the Cuis clones were involved in Sheyvan's betrayal, Darth Vader became strongly opposed to using the Cuis line further, as well as any Forceful template. The failed rebellion, however brief, convinced him that Force-sensitives—and even clones of Force-sensitives—were naturally inclined to seek more power by betraying their masters, especially if they relied on the dark side of the Force. As a result, he chose to limit clone lines to ordinary candidates. The Stormtrooper Corps continued to use clone soldiers, but none after the Cuis clones were created from a Forceful genome.
Although Vader had long abandoned the idea of "Force-sensitive stormtroopers," he was forced to rethink his position against cloning a Forceful template after the death of his former apprentice, the pseudo Sith-turned-Jedi Galen Marek. Using the apprentice's preserved body as a template in the Timira City Cloning Facility on Kamino, Vader conducted an experiment to create the perfect clone of his fallen disciple—a more powerful and obedient version of the original Starkiller. Unlike the success Vader had experienced with creating stable clones from the Cuis line, the Marek template proved almost impossible to replicate without encountering many setbacks, forcing Vader to repeat the procedure several times to gradually correct the errors in the experiment. Scientists were confused as to why it was so difficult to clone a Forceful being, although some experts—such as Ni-Ke-Vanz, a Rebel medic—suggested that the Force was somehow responsible for disrupting the stability of clones created from genetic donors with high levels of midi-chlorians in their cells.
Aside from the genetic flaws, the Marek clones differed from their Cuis predecessors in another way—they were all trained using memory flashes, which allowed them to inherit their donor's skills, but also Marek's emotional attachments that Vader blamed for weakening his former apprentice. With the exception of a single test subject, every clone of Marek was unable to distinguish his own thoughts and memories from those of his originator, which led to identity crises and ultimately insanity.
In the commentaries for the Special Edition, George Lucas mentions that in his initial ideas for the saga, lightsabers were common weapons throughout the galaxy, but he later decided to limit them to the Jedi. Based on Lucas's original concept, Ralph McQuarrie created concept art of lightsaber-wielding stormtroopers for A New Hope. This was referenced in the image above in the pose of the stormtrooper to the right of Darth Vader.