The factories were designed to build Dark troopers to support Operation Dark Disease, which was a military campaign in the Dark Order War against the New Republic. Most of the factories were underground, while the entrances and several landing pads were visible on the surface. Their construction was begun in the year 14 ABY in preparation for Operation Dark Disease. They were finished shortly before 15 ABY, in time to produce enough Dark troopers for the attack on Coruscant.
Since the Infector, the Imperial Factory ship responsible for transporting the Dark troopers was incapable of producing the droids fast enough for the well-timed attacks of the Operation, the Bakura Factories were needed to assist in their construction. After the factories were active, Dark troopers became a common sight inside the military bases throughout Bakura, as well as in some of the planet's cities, patrolling the streets, assisting stormtroopers in questioning citizens, or standing guard during investigations.
During the Second Battle of Bakura, The factories were pounded into molten slag by orbital bombardment from Darth Persia's fleet, which eventually destroyed the surface of the planet. All Dark troopers on the surface were destroyed, and only a small handful of them at best were off-planet at the time of the bombardment. As a result, the Dark troopers quickly returned to the staggeringly low numbers that they had previously in the Galactic Civil War. When the Dark Order of Korr was overthrown by the Sith, Darth Persia decided that although the Dark troopers had proven themselves to be highly capable war machines in the past, their high cost made them an unneeded addition to his armies. Therefore, most of the Phase 1 Dark troopers were dismantled and the rest were left to guard important locations, such as the Eriadu City Palace.