The Black War was a colloquial name for the phase of the Rebellion when the factional governments stopped believing they could win the war through attacks on their opponents' military forces and facilities. They switched the focus of their attacks to critical civilian infrastructure, so as to deny its use to their enemies (on occasion, destroying infrastructure in space they themselves controlled but believed they could not hold in the long term).
Prior to the year 1122, the various factional governments believed that they could "win" the war and be recognized as the legitimate ruler of the Imperium, or have their governing philosophy be the guiding force behind a reunited Imperium. To this end, they restricted their military activities largely to enemy fleets and military targets, avoiding targeting civilian infrastructure with the hope of controlling it after their victory. This is known as a counterforce strategy.
In 1122, the factions came to the conclusion that their best hope was to avoid "losing" the war and to preserve themselves as intact and independent entities. To that end they began a countervalue strategy, attacking civilian infrastructure such as civilian starports and critical life-support systems on marginal worlds. The aim was to deny the use of this infrastructure to the enemy, since there was little hope of bringing it under their own control. One of the first such attacks was on Susadi in Gushemege sector on 267-1122, when Lucan's forces attacked and severely damaged the class A starport there.
The effect of the Black War was to shrink the core areas of all of the factions, leaving large areas between them as "Wilds" with reduced populations, degraded interstellar travel capabilities, and no loyalty to the former Imperium or the various factions. Planets without habitable biospheres (e.g. those with no atmosphere or a fatal atmospheric taint) were especially hard hit, many losing their entire populations when the infrastructure critical to supporting life was destroyed.