The Qelipoth was a group of ten enormous Reapers, all linked together to pool their already-considerable powers. According to the Reaper-exile called Apollyon, the Qelipoth were living relics from the long-forgotten time when the Reaper fleet was small and confined itself to a handful of systems. In those days, the Qelipoth served as a sort of beit din among the Reapers, determining what direction the fleet should take. Those who argued against the Qelipoth, who preached "heresy", were obliterated or exiled to distant stars and planets.
As the millenia passed, the Reaper fleet grew, and most of the Reapers evolved to become nations within themselves, thus rendering a governing body like the Qelipoth obsolete. By the time they banished the Reaper-exile to Uke Mochi, most of the fleet had dispersed, its members having travelled beyond the Qelipoth's reach, which had not been designed for interstellar travel. Apollyon speculated that the Qelipoth were still out there; since the Reapers' repeated destruction of organic life has shown that history tends to move eliptically, the Reaper-exile believed that one day the Reapers themselves would be reduced and forced to once again confine themselves within the Qelipoth's reach, thus renewing the Qelipoth's purpose.
In fact, the Qelipoth had been slowly dying of energy starvation, and its members had long since gone into stasis. This was broken in 2185 CE, when Apollyon attempted to indoctrinate all sentients on Uke Mochi. Its attempt failed, and the local military sentenced it to be destroyed. Realizing that its time was short, the Reaper-exile focused all its remaining energy into indoctrinating a single human, James Skinner, a criminal genius who had been forced to devise a way to kill Apollyon as part of his sentence for his crimes. By the time Apollyon was finally destroyed in 2187 CE, Skinner had been thoroughly indoctrinated, and unleashed an apparently lethal plague. During the resultant emergency, he was evacuated aboard the SSV Belgrade.