As it was, Slovenia and Croatia made it out as new nations after a brief struggle, as did Macedonia later, but the primarily Muslim sub-states of Bosnia and Kosovo came into prolonged conflict with Serbian military and paramilitary forces. Everyone engaged in ethic cleansing and atrocities to some degree, but the Serbs got the blame for being the aggressor and doing more of it than their adversaries.
Other powers and forces were involved, of course, but I am not sure what you mean by "far larger things at play." I am willing to hear your views.
That goes way back to that part of the world fighting against the ottomans. Wherever moslems go, death and chaos follow.